If the file is a version with a virus - then you dump the whole file!
This is in addition to the other things an anti-virus facility would do to render it ineffective. That may mean leaving some virus code in place, though broken.
The guys who write virus grew up playing "core wars". The way a virus ends up buried deep among executables, and maybe using parts of the drive not normally addressable by the system is bad enough. A virus living by doing its actions as part of legitimate and essential other services it hijacked, and capable of re-spawning and re-embedding itself if attacked, is a very difficult thing to kill.
Antivirus software may not have any clear way to identify the virus in a file, other than to know that the digital signiature checksum indicated it was carrying "extras". Especially if it was the kind of indirect code that writes other executable code, you can see why you should obtain a clean copy.
The antivirus software may be capable of cleaning out the virus, but needs also to throw out the original source of infection, or it will just have to do it all over again later.