...without creating a NFTS (or whatever is the exact acronym)

I had my installation files copied on my hard drive, thought it would speed up the installation, but when i'm starting the DOS install program, it says the hard-drive is not Windows 2000 compatible. I do NOT want to create a new partition or format my hard-drive just to please a new OS. How can i do ?
Would it be because the files are located on /windows/desktop/ and it wouldn't want to touch the windows directory ?
(i would have used the CD, but it fell on the ground and the lovely cats were playing, and now there's a big lovely ray that makes it unreadable)