If the drive's infected, install and run a virus detection program like Norton Antivirus. Then you can determine which programs/data were affected, if any, and reinstall those. No need to reformat the drive unless it's so screwed up that nothing works, but even then there are utilities to try to recover startup info and data.
Give a man a fish, he'll eat for one day. Teach a man to fish, he'll drink all your beer.
Cheers, Jeff (SCJP 1.4 all those years ago...)
To format partition: You have the Win2000 installation CD? Than just pop your CD in, than boot your computer (make sure you have configured the BIOS to check the CDROM first, if it detects any bootable app) and than just follow the instruction.
If your OS (Windows) is installed in C:, you cannot format it in Windows. By formating that drive, you need to understand that all your installed applications & data will be gone.
As suggested, it would be better to use an anti-virus software to determine if its infected by virus(es). If you're worried that your installed anti-virus software had too been infected, go get your system scanned for free online here.