After defraging hard drive on network some programs don't work

I'm working with some rather old machines, the OS is 2000 professional. The machines have only 64 mg mem. and about 8 gig hard drive. While I was getting the information I needed to add memory, I noticed that the drive was a mess, so I defraged the hard drive; now some of the programs don't work. Is there anyway to fix them without reinstalling the programs?
Your help on this matter is greatly appreciated.