fat vs. ntfs

hi,
I am getting ready to upgrade from nt4.0 to win2k server. I have recently promote the server that I want as my active directory server. My situation is the following, my bootable drive is c: and for some reason it is formatted FAT. The other drives are NTFS. Is there any way that I could format that drive NTFS, without having to do a fresh install.
Is it recommended that I implement a new installation, instead of an upgrade? Keep in mind that I have been anticipating an upgrade, until Irealized that the bootable drive is FAT. I had everything ready for that upgrade but it does not seem as the best solution. Give me some advise. cn