NDD can't fix trashed drive

I have a damaged drive in which the Program Files directory and a few other directories just dissapeared. When I used scandisk (DOS) and NDD, they both said that I did not have enough memory to continue even though I have 256 megs of memory. What can I do to fix the FAT without formatting the drive  since i still have files and folders that I still can access and can't back up right now.

You can copy everything and rescue it to another drive, using Seagate discwizard.

But how can I repair the partition , even if it's just to get the
file space back?