You can format the drive, which Win2k resides on. Use the convert option kyoshozx has shown you. It will tell you it?s not able to convert, but it?ll also ask if you would like to convert at a later time, after restart, just select yes. The next time you restart it will convert your C: driver to NTFS.
You will not lose any data. But there is no reverse process, meaning you can?t convert back to FAT/32.
If you want to do a clean install then repeat the installation process for Win2k. In there you?ll be able to delete partitions and format them for NTFS.