There are several ways a virus can infect a file. It could append it's self or it could just copy over certain parts. If the virus overwrites the original file, you'll need your backups.

First is to identify the virus, this will make life a lot easier. Find out what you can about how the virus infects the file. Then you can think of ways to remove it. You can basicly use any language you're comfortable with to write your own remover.

You're off to the deep end if nobody knows the virus. You'll need to have a good understanding of assembly and the C/C++ stack to make sense of it all.