Personally I would use a GParted Live CD (http://gparted.sourceforge.net/livecd.php).
Once you burn the .iso image to a blank disk (using the Windows Disk Image Burner), you can boot into the CD and have complete control over formatting and partitioning your hard drives. You can even set disks as "unformatted" or format them as Linux file systems (ext4 etc.). If you want to simply reinstall Windows and format your drives as NTFS then the suggestions by the other posters on this thread are probably easier though.
P.S. Make sure your data is backed up in case you haven't done that yet.