psilocyberin said:

If you are talking about real audio, like from a CD, I'm pretty sure that is impossible as of right now. The only thing close to that would be to slice out certain frequencies.

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Actually EQing to get out some instruments it's not as difficult or noneffective as it seems. It is quite reasonable to the extent that there will always be some harmonics that will remain there and that you could unintentionally take out some other things. (although you're completely right in that it would be impossible to mute an instrument completely without affecting the rest of the mix)

As a rule of thumb is very hard to take out completely a sound, but the less instruments on a give sequence and the more precise EQing/frequency muting you can do (it's more about effort than programs) the better results you could get.

I.E. a guitar track on a Lenny kravitz song would be horrible to take out and it would completely destroy the vocals, part of the bass and so on.
On a techno track you could take out almost completely the crash of a drum set and only notice a little roll off on the highs of the track.

I would recommend for you (original poster) a program that can perform parametric and hopefully para-graphic EQing, and some muting of certain frequencies (I forgot how that is called, but I could search it if you want) for the best results. Also a bit of theoretical knowledge about the specific ranges of each instrument would be nice.

I hope that was somehow useful, and please excuse my English, I'm not that good when it comes to technicalities