Here's something I just found.
I was using CMEdit to copy/paste creations from a couple of worlds into a superflat world, when I noticed this had pasted in the original biomes. I copied a huge flat slab of grass from the superflat world and pasted it above the imported builds. This altered the biome to "plains". I then just filled the grass "roof" I had created with air.
It's all good now. In the future, I'll just uncheck that little box marked "Copy Biome" before I paste stuff, but it's a happy accident.
So you still need MCEdit, but you can do without the plugin.
Hope this helps someone.