Try MCMapdeleter: viewtopic.php?f=25&t=26733
I'm not sure if MineCraft generates new ground at empty spots. If it does, then I can't suggest anything else but MCEdit (It's quite easy if you read manual, but can get sometimes laggy).
The game will regenerate terrain in the areas that are deleted by mcmapdeleter. Unlike MCEdit, it completely deletes generated chunks from the world instead of "blanking out" the existing chunks. When the in-game mapgen sees deleted chunks, it will recreate them. I've used it quite a bit and do say that you get some interested terrain when it regenerates the land (i.e. sheer cliffs, etc. similar to a chunk error).