Cactus Music has the best reply of the thread so far. More info about the specifics of the problem are needed before any kind of meaningful answer can be offered. All the other answers given are potentially good solid suggestions. But all of them are based on assumptions about exactly what the problem is.
Is it fret buzz? Is it AC hum? Is it faulty wire crackle or pot dirt? Is this a stereo recording or one track of a multi-track recording?
If its an acoustic track on that is part of a multi-track recording and its only in one or two places on the recording, choice 1 for me would be to find a good version of the chord/note/song part in question earlier or later in the track and copy/paste over the bad stuff. Choice 2 would be to just redo the acoustic track or (if it works aesthetically) lose the acoustic in the section where the bad stuff is.
If its a stereo file, then the answers already given would apply. But depending on the problem its possible that nothing short of a new recording will do much to fix the situation.