Always run SFC for problems like this. It's easiest to run from within windows. Open a command prompt and type is sfc /scanow, hit ENTER. SFC will fix any problems with the operating system files.
If you can't get to windows, put in your windows disk, boot to it and choose REPAIR from the options. When you get to the command prompt, type in:
sfc /scannow /offbootdir=c:\ /offwindir=c:\windows
Once you get windows up, open windows explorer, right click on your C: drive>PROPERTIES>TOOLS>CHECK NOW. It will ask if you want to schedule a disk check on reboot, say YES. Reboot the computer and let it run.
Often, missing files are a sign of a failing hard drive , malware or viruses. You should run full virus and malware scans. If those are clean, then determine which brand of hard drive you have and download their diagnostic tool. Run a FULL CHECK of the hard drive and then you'll know if you actually have a hard drive problem.