WorldEdit and MCEdit can change the biome of a selected area, but they don't actually change the shape of the landscape and the plants and other blocks in them to fit the new biome type. For example, when I change a "Mountain" biome to a "Plains" biome, the resulting "Plains" still have mountains in them and spruce trees.

So if I want to replace not only the biome type, but also the shape of the landscape that goes with that biome – so that after the change the area appears as if the world had been created with the new biome instead of the old one –, how do I do that?