procedural generation - How is a 3d perlin noise function used to generate terrain?

I can wrap my head around using a 2d perlin noise function to generate the height value but I don't understand why a 3d perlin noise function would be used. In Notch's blog, http://notch.tumblr.com/post/3746989361/terrain-generation-part-1, he mentioned using a 3d perlin noise function for the terrain generation on Minecraft. Does anyone know how that would be done and why it would be useful? If you are passing x,y, and z values doesn't that imply you already have the height?

Answer

2D perlin noise is good for height maps, but in this case it seems that he is not using a height map. Instead he has a 3D grid, where any cell can be empty. This allows caves and such formations, where the ground height is not a single value for given 2D location.