I think you'll need to boot into some bootable disk (cd, floppy, other hd, ...) because you won't be able to fully access your main disk when you're working on that one... Then you have to remove all partitions from your hd, and format it. Finally just reinstall windows and you're ready.
If you don't have a bootable disk at all, you could download the Ubuntu live cd-thingie and use that to boot up (the advantage is that you still have an os, while you don't need your main hd.)
Here is where you can download the Ubuntu live cd:
http://www.ubuntu.com/getubuntu/download