Agree with mr DB, if in doubt format the drive/s.
Make and save anything you want to keep inc registration codes for programmes, favourites, emails, piccies, etc I use an external USB drive but used to do it on rewritable cd.
The cd/dvd will be detected upon a clean install. May need to swap the bios setting over whilst installing windows. Probably hard drive is first boot, change to cd then hdd as 2nd boot device, unless you need a floppy as first boot.
While your at it you could clean the inside, a source for a number of problems.