Structure

Every specific group of blocks purposefully formed in Minecraft based on coding is part of a natural structure.

The Overworld
The Overworld contains numerous generated structures, at a wide variety of scales.

Terrain
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.

Mountains
Mountains are hills with extreme slopes. 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.

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. Floating Islands are usually found in the mountain and Mushroom biomes, but can be found anywhere.

Oceans
Seas/oceans are huge bodies of water with every single water tile being a spring. 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.

Rivers
Rivers are long strands of water that cut through or seperates biomes. They have no current. Rivers have also been known to be a reliable source of clay. In hilly or mountainous areas, the ground can rise above layer 62, producing a dry riverbed.

Hills
Hills are randomly generated pieces of land in the map. Like stairs, hills are always traversable to their lowest point by virtue of the algorithm which generates them; there is 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.

Beaches
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.

Top 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.

Basins
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.

Caverns
Caverns are caves and tunnels that are automatically generated under the ground in various places. Caverns are composed mainly of stone, and contain small amounts of ores. For more details, see the Caverns article.

Ravines
Ravines are tall, long cracks of air, about 5-20 blocks in height. The width is barely a few blocks, usually no more than 5, sometimes making ravines hard to navigate from below. Ravines can have small ledges along the top, which are possible to travel along. Ravines can be found at any level, and also scarcely appear on the world surface, forming canyons. Such canyons do, from time to time, appear underwater where safe entry is possible.

Ravines can connect to caves, dungeons, abandoned mines, and any other generated structures. Due to the large surface area of their walls, may also have water/lava flowing down them (either from a spring or an underground lake of the lava/water).

Abandoned Mine Shafts
Abandoned Mine Shafts are structures generated underground that consists 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. According to players, it is extremely easy to get lost in the labyrinth if you don't place torches or reminders. As of Minecraft 1.2, open areas generate with bridges instead of leaving floating platforms. They contain chests that may have rare items such as diamonds and melon seeds, the latter only being found naturally in mine shafts. They may also contain iron ingots, coal, pickaxes, and other useful items. They are likely to expose veins of coal, iron, and gold ore, and rarely, lapis lazuli and diamond ore.

NPC Villages
NPC Villages are generated on flat lands and are a site for NPC Villagers. They are composed of several different houses, farms and often a smithy and/or a tower. Sometimes the blacksmith of the village may have a chest with some useful items in it, such as diamonds or iron tools and armor. The Villagers move about in the area around the village. They are the only structure to generate on the world type Superflat, and being that they require large amounts of flat land, this makes them more abundant. Thus, 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).

Strongholds
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, and iron bars 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, and compasses.

Small Structures
The quantity of most of these features (aside from lakes, mineral veins, and springs) is biome-dependent; not all of them can be found in every biome.

Lakes
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, 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.

Dungeons
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 chests may contain rare valuables, such as cocoa beans, music discs, saddles and golden apples. Rarely, there may be two dungeons generated right next to eachother, 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 the dungeon not containing a monster spawner at all, giving the player a chance of free goods early in the game.

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, and Lapis Lazuli. They can only form in Stone, and do not replace each other or any other block.

Trees
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 in the Minecraft 1.2 update, jungle trees may be found. Saplings can be grown faster by using a bone meal on them.

Huge Mushrooms
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.

Plants
A variety of smaller plants may be generated: Flowers, Tall Grass, Dead Bushes, Lily Pads, Mushrooms, Sugar Cane, Pumpkins, and Cactus.

Springs
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 1.2.1, 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. 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, such as in the seed 6772646013745403867, at 1705, 170.

The Nether
The Nether, though equally vast, contains far fewer types of generated structures than the Overworld.

Lava Sea
Lava Seas are, as the name suggests, great oceans of lava which 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 of meters in any direction, and are usually bordered by netherrack (or more rarely soul sand). In some instances these "seas" have been known to cover an area so vast that attempting to cross is nearly impossible.

Nether Fortresses
Nether Fortresses are very large complexes made mainly of nether bricks. Due to this, it is very easy to get lost in them and hard to navigate back to your portals. It is recommended that you use "breadcrumbs" to find your way back. Nether fortresses can often tunnel through netherrack, and the inside of the tunnels will be cleared of netherrack by the terrain generator. You can find Blaze spawners in balconies and nether wart inside.

Glowstone vein
Glowstone veins are one of the hardest natural materials to harvest. They form on the underside of Netherrack, so they are most often found near the ceiling of the Nether, where a fall is often fatal.

The End
The End is the most barren dimension, with only two significant structures.

The Island
Most of the End is a large island composed entirely of End Stone, floating in an endless void.

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 you can see without digging. Ender Crystals will spawn on top of each one to heal the Enderdragon.