Cleaning two audio files of the same thing?

Can you (i.e. is there a program) that can take two digitized copies of a song from, let's say two different copies of the same album, compare the waveforms and come up with one clean version of the song (pops and clicks and general noise in one copy won't be in the other copy, yes?)? If so, how about if they have already been MP3'ed and are not WAVs?

Thanks!

Bob

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