If you are certain that a cracker (the word "hacker" is misused in this context) has changed some files on your disk, then you don't really know how much he's changed. If he's skillful, he's designed his breakin so that you'll hope you can fix just the programs that seem wrong, but he's also designed his breakin to modify programs that you might not consider. Programs like these:
If your system's behavior is of any interest to you (and it had better be if that system is connected to the Internet, because there's a good chance the system has become a spambot, which makes the rest of us want to breathe down your neck), you'll boot an emergency CD, back up your user data, and reinstall from scratch.
This is very important.