Every specific group of blocks purposefully formed in Minecraft based on coding is part of a natural structure.
The Overworld contains numerous generated structures, at a wide variety of scales.
Biomes dictate the shape and height of the world. At this stage, the ground is made entirely of stone, with water filling in any empty space below layer 63, with exception for structures.
Mountains are hills with extreme slopes and cliffs. Prior to the Adventure Update, these highly mountainous landforms were found in all type of biomes, but from the Adventure Update onwards are very rare outside the Extreme Hills biome. They were generated as part of the terrain generation algorithm.
A picture of an extreme hills biome
 Floating "islands"
Floating "islands" are structures that float in midair that are not connected to the ground, the sea, hills or cliffs. Floating "islands" are normally just random pieces of floating dirt and stone found near cliffs, but on rare occasions they can be large, floating structures that even have springs and trees on them. They are actually the result of a bug which could prove to be challenging to fix, when a tall terrain is generated on top of another node of equal importance (such as a cave or a lava pool). However, due to their generally well perceived appearance, the developers at Mojang chose to embrace them as a part of standard level generation. Floating Islands are most frequently found in the Mountain, Tundra, ice mountains and Mushroom biomes, but can be found anywhere. In Multiplayer, they can be a useful place to put your base because they can be hard to reach.
Oceans/Seas are huge bodies of water with every single water tile being a source block. The ground can rise high enough to produce small, relatively barren islands. Prior to the Adventure Update, oceans were generated as part of the terrain generation algorithm, but since then they are part of the Ocean biome.
A picture of an Ocean biome
Rivers are long strands of water that cut through or separate biomes. They have no current. Rivers have also been known to be a reliable source of clay. In hilly or mountainous biomes/areas, the ground can rise above layer 62, producing a dry riverbed.
The first image of a river released by Notch, with a Huge Mushroom next to it. (Note: Huge Mushrooms don't spawn naturally outside Mushroom biomes)
Hills are randomly generated pieces of land in the map. Like stairs, hills are always traverse-able to their lowest point by virtue of the algorithm which generates them; there is almost always a place on each level from where the next level can be accessed, meaning that the player can climb a hill one level at a time until they reach the top. Cases where this is not true are rare.
Beaches usually generate next to oceans and cover all nearby shorelines. They used to come in two varieties: sand beach and gravel beach. Sandstone is located below sand in sand beaches. Gravel beaches had no such border and thus pose dangers like falling into caverns located right underneath them.
Historical notes: Due to the changes in the terrain generation algorithm in the Beta 1.8 beaches were removed completely from the game. However, as of Snapshot 12w01a and update 1.2, sand beaches have made a return, but the way they look and generate are not the same as before. Gravel beaches did not appear at all in 1.1. After Snapshot 12w07a, the generation of beaches has been greatly improved.
 Surface layers
The uppermost layers of the terrain are converted to a biome-dependent material: usually grass and dirt, or sand in deserts and beaches. Sandstone is generated under sand.
Occasionally, instead of being converted to dirt or sand, the top layer is stripped away, leaving a 'Basin' of bare stone. There is a common misconception in the community that these are errors, however they are an intended feature. They bear some resemblance to a geological 'shield' (an area of tectonically stable rock that has been exposed to prolonged erosion due to its very old age; it is distinct from the geological term "basin"). They seem to be more common in Forest or Plains, and are sometimes seen filled with water. Sometimes, common minerals can be found on the surface such as coal and iron ore.
 Large structures
- Main article: Cavern
Caverns are caves and tunnels that are automatically generated under the ground in various places. Caverns are composed mainly of stone, and contain large amounts of ores. In caverns underneath deserts or beaches, you can see sandstone stalactites.
A dark cave with a zombie
Ravines are tall, long cracks of air, usually measuring around 30 to 50 blocks in height, making them quite dangerous if one should fall down. However, they are narrow, usually no more than 5 blocks wide. Ravines can have small ledges along the top, which are possible to travel along. Ravines can be found at any level, and also sometimes appear on the world surface, forming canyons -- a serious hazard when wandering around the countryside, as they may not be obvious until you're right at the edge... or over it. Such canyons do, from time to time, appear underwater, and there safe entry is possible. They can go very deep underground, sometimes spawning slimes or exposing diamond ore. If they reach deep enough, they may also be floored by the lava lakes at level 10.
Ravines can connect to caves, dungeons, abandoned mines, and any other generated structures. Due to the large surface area of their walls, ravines often have water and/or lava flowing down them (from springs in the walls, underground lakes, or even openings to the sea). The player can also add their own waterfall(s) from the edge, to descend more-or-less safely (watch out for lava and monsters).
 Abandoned Mine Shafts
- Main article: Abandoned Mine Shaft
Abandoned Mine Shafts are structures generated underground which consist of branching mining tunnels with wooden supports, and broken rails passing through it. This is also the only place in Minecraft where venomous Cave Spiders can be found. It is easy to get lost in the labyrinth if torches or other reminder blocks are not placed. As of Minecraft 1.2, open areas generate with bridges instead of leaving floating platforms. They contain chests ( or of 13w02a Minecart with chests)that may have rare items such as diamonds and melon seeds, the latter only being found naturally in mine shafts (melon seeds can now also be obtained by trading with villagers for melon and crafted into seeds). They may also contain iron ingots, coal, pickaxes, and other useful items. They are likely to expose veins of coal, iron, lapis lazuli, and gold ore, and rarely, emerald and diamond ore.
 NPC Villages
- Main article: NPC Villages
NPC Villages are generated in Desert and Plains biomes and are a site for NPC Villagers. The word NPC stands for Non Playable Character. They are composed of several different houses, farms and often a blacksmith and sometimes a tower or two. The Villagers move about in the area around the village. Villages change appearance and composition depending on the biome they are located in. In a normal world NPC Villages are most common in Deserts because it is the flattest biome (after oceans, which is not possible to have NPC villages generated on).
- Main article: Stronghold
Strongholds are structures that contain multiple rooms, doors and other aspects. (Some of these rooms include libraries, fountain rooms, dungeon-like rooms, etc.) stone brick, mossy stone brick, cracked stone brick, doors, iron bars, and stone slabs are the materials that make up the strongholds. They also contain silverfish, which one should be careful of when digging around in strongholds. Portals to The End are found in specific rooms in strongholds. Chests may be found containing items such as books, Redstone, Eye of Ender, apples, bread, compasses, and iron tools/armor.
 Small structures
The quantity of most of these features (aside from lakes, mineral veins, and springs) are biome-dependent; not all of them can be found in every biome.
Lakes are small bodies of water in which the player is able to swim, and are a large collection of water spring blocks. Lakes can now be generated above sea level or inside caverns, and are small bodies of water surrounded simply by dirt. When in a winter biome, these small lakes are never initially frozen but can turn to ice. These lakes can also be composed of lava; however, lakes of lava are more rare. Lava lakes found at the surface may be surrounded by gravel, sand, stone, and coal ore.
Prior to 1.2, it was possible for lava lakes to spawn 1 block above bedrock, removing the bedrock and replacing it with stone (which on survival could allow access to the void). These were quite rare and difficult to find. As of 13w17a, water oases no longer generate in deserts.
- Main article: Dungeon
Dungeons are small, mostly underground, one-room spaces bordered by moss stone and cobblestone, and typically contain chests with rare items, and a hostile Monster Spawner in the center, which guards the chests. The monster spawner can spawn either zombies, skeletons, or spiders (the last will include occasional spider jockey). The chests may contain rare valuables, such as music discs, enchanted books, saddles and golden apples. Rarely, there may be two dungeons generated right next to each other, this can make two dungeons in only about one space. There have also been reports of three or more dungeons in very close proximity to each other. There is a small chance of not getting a chest.
 Mineral veins
A mineral vein is a natural deposit of ores. Players can come across these veins in caverns or anywhere where there is natural stone. Underground deposits of dirt and gravel are generated in this step, followed by the more precious ores: coal, iron, gold, Redstone, diamond, emerald (in extreme hill biomes 1.3.1) and lapis lazuli. They can only form in Stone, and do not replace each other or any other block.
- Main article: Tree
Trees are structures created both by the automatic generation of the map and by players (they grow from saplings). They are made of wood and leaves. Trees can range from small trees, often found in groups, to large trees that may require several minutes to harvest. In Beta 1.2, birch trees and pine trees may be found, and as of the Minecraft 1.2 update, jungle trees may be found. Jungle trees can naturally grow more than a single block thick and have vines growing on them. Cocoa plants can be found, planted and harvested on them. Saplings can be grown faster by using a bone meal on them.
 Huge Mushrooms
- Main article: Huge Mushroom
Huge Mushrooms are structures that only naturally occur in mushroom biomes. They are composed of mushroom stalks and either red or brown colored blocks for the cap. They can be grown outside Mushroom Islands by fertilizing red or brown mushroom with bone meal, or can be generated with mycelium.
A variety of smaller plants may be generated: flowers, tall grass, dead bushes, lily pads, mushrooms, sugarcane, pumpkins, cactus, ferns, vines, and cocoa plants. Occasionally both red and yellow flowers may be found in clusters of their own colour.
Springs are randomly generated blocks of either lava or water that act as a source of their respective material. While both can be found on the vertical side of stone blocks above the surface, lava springs are more often found underground beneath layer 32 in caverns. Both of these sources can be collected and moved via the use of buckets. Springs can only be found in versions from Infdev onward, as fluids behaved differently in older versions.
 Desert wells
First introduced in 12w04a (snapshot of 1.2), these well-like structures built of sandstone blocks and slabs generate only in the desert biome. Although assumed to be wells, their exact purpose and function is yet to be known. A proposed reason would be for filling buckets with water, since the middle water spring is infinite. Also, it is possible for a well to spawn over a stronghold or an abandoned mineshaft. They have a 1/1000 chance to be generated in any desert chunk, which makes them a rare sight. It is possible for a well to generate around a cactus. The well structure can also spawn even with the "Generate Structures" setting disabled. As of 13w17a (snapshot of 1.6) water lakes no longer generate within deserts, thus making desert wells (and desert village farms) the only "natural" source of water in desert biomes.
Temples are a kind of naturally generating structure. They contain treasure, but they also contain traps and puzzles.
 Desert Temples
- Main article: Desert temple
Desert temples are a type of structure that occurs naturally in desert biomes as of snapshot 12w21a (snapshot of 1.3). Also known as pyramids, they mostly consist of wool, sandstone, chiseled sandstone, smooth sandstone and sandstone stairs. In the middle of the pyramid is a block of blue wool. Underneath it is a chamber where the player can find 4 chests which contain very valuable loot,(Although the most common loot is gold and zombie flesh) and a stone pressure plate connected to a 3x3 grid of TNT. Some treasures found in Pyramids include emeralds, diamonds, iron ingots, gold ingots, rotten flesh and bones. In version 12w23a of the game it was possible for pyramids to spawn in the jungle. The orange wool on the side of the towers resemble the Egyptian hieroglyph called the ankh, which is the symbol for life.
 Jungle Temples
- Main article: Jungle Temple
Jungle temples are structures added in snapshot 12w22a (snapshot of 1.3). They contain arrow traps and hidden treasures. Jungle Temples use tripwire to activate dispensers. There is also a lock made up of pistons, levers, redstone, and redstone repeaters. When correctly operating the lock, a hatch will appear on the main floor just above it, leading to another chest. Instead of figuring out the combination, you could also dig through the wall where the levers are and get the chest.
 Witch Huts
Witch Huts generate in swamp biomes or, very, very rarely, other biomes. Witches can spawn inside of them. The huts consist of spruce Wood Planks and oak wood. Spruce wood stairs make the roof borders, 2 fences decorate the entrance and one fence make the entrance window bars. Inside is a crafting table and an empty cauldron; on the windowsills are potted mushrooms. There's no valid way a witch can get back up into the hut if it falls off it. There are no chests or any other loot inside. It is possible, but rare, for a mushroom to generate inside the Hut while not potted, with the potted one still in place. Strangely, they are just high enough for the witches to fit in, but their hats are in the ceiling, making the animation look broken. They seem to be based on the design of Baba Yaga's hut, a witch from Slavic folklore who lived in a hut that walked around on giant chicken legs.
The Nether, though equally vast, contains far fewer types of generated structures than the Overworld.
 Lava sea
Lava seas are found at and below level 30 in the Nether. They make a large portion of the Nether, and are extremely common. They can stretch for hundreds, if not thousands, of meters in any direction, and are usually bordered by Netherrack (or more rarely soul sand). Even on far render distance, the player is rarely able to see the other side of the seas due to their vastness.
A lava sea with Ghasts taking a dip in it
 Nether Fortresses
- Main article: Nether Fortress
Nether fortresses are very large complexes made mainly of nether bricks (with added nether brick fences and stairs to be found). Due to this, it is very easy to get lost in them and it may be difficult to navigate back to portals. Nether fortresses can often tunnel through Netherrack. and the inside of the tunnels will be cleared of Netherrack by the terrain generator. Blaze spawners and nether wart farms are only found in Nether Fortresses. Aside from the spawners, Blazes can spawn anywhere in the fortresses, and there are also not only Zombie Pigmen, but Wither Skeletons as well. As of 13w18b (snapshot of 1.6), Nether Fortresses have loot. The chests with loot are usually generated in corners.
A nether fortress generated in the Nether
 Glowstone vein
Glowstone veins can be among the hardest natural materials to harvest that don't require digging. They form in coral-like structures on the underside of hanging Netherrack, so they are often found on the ceilings of the Nether, where they provide light along with the ever present lava. Luckily, there are places where the ceiling is very low, and veins there can usually be mined without undue risk.
There are areas of soul sand and gravel around layer 64, and as of the 1.5 update, there is nether quartz ore and "hidden lava", which is a single block of lava in random places not visible without digging.
The End is the most barren dimension, with only four types of significant structures.
 The island
Most of the End is a large, asteroid-like island composed entirely of End Stone, floating in an endless void.
The fountain is found once the Ender Dragon is defeated, giving the player a way back home. This fountain is also the foundation of the Ender Dragon egg.
 Obsidian platform
The obsidian platform is a 5x5 square of obsidian where the player spawns once the player enters the End.
- Sometimes the platform spawns inside a case of Endstone. It will delete enough Endstone so that the player can walk around.
- Occasionally the platform will spawn in midair.
- Very rarely, the platform will spawn on an obsidian pillar and have an Ender crystal on it.
 Obsidian pillars
- Main article: Obsidian Pillars
Obsidian pillars, or obsidian spikes, are tall, tower-like structures that generate in The End. They first appeared in 1.0.0 with the introduction of The End. No part of them are in the ground; there is no obsidian below the lowest block of obsidian that the player can see without digging. Ender Crystals will spawn on top of each one to heal the Ender Dragon.
- Main article: History of biomes and generated structures