Win 2000 Remove and reinstall

"saturated with files of a unknown origin "
Sounds like a virus, during the install of win 2000 you can choose to delete the partition, which in normal circumstances would be sufficient.
However, if your hard drive's mbr is infected this will not be enough. All of the hard drive manufacturers in clude a floppy whith their hard drives when sold, that will remove this MBR. It is based on a program commerially available called DRIVEPRO. See if you can find a copy of this and use it. They want about 70 bucks on the net for the program, but that is what a 20 gig hard drive costs anyway, so guess what I would choose. Let me know what hard drive manufacturer it is and maybe i have a disk left over (maxtor, wd, seagate). Or a really good virus software will clean up your drive. (shameless plug here)
http://my-etrust.com/products/info/Antivirus/2

The easiest solution to clean install is to FDisk your system. You can completely delete the partitions and recreate them from a pristine drive. You will of course need to repartition and reformat afterwards. I'd Fdisk the MBR as well...

That said, I would try to track down those unknown files first. You may have to deal with a virus problem etc...and if it has affected your media (floppies etc) or other networked systems (if any) you may end up right back in the same boat. There are many other possibilities (configuration issues, etc) and if you give us some details about the files, maybe you can resolve the problem without nuking the whole drive...

Good Luck!

You can download a small utility from most hard drive manuf.websites called clearhdd. It is only 10k so you can fit it onto any boot floppy. It will clean a hard drive to the same condition that the factory sells it as.
Good luck!

Mike