I'm beginning 11-12 music next year (I'm a bass player) & I was wondering if their are any downloadable/purchaseable programs which can isolate bass or guitar lines, mute them or even take them out perminantly. I've seen lots of effects pedals which can do this but was wondering if their was a program for doing it to mp3s.
Never heard about it. I know that there are programms which can isolate voices on songs but I'm not so sure if they are going to work with bass parts because the frequencies interfere with the base drum very often.

At least that's what I think - I'm no pro...
You won't be able to do it, it's sort of like taking a picture and then trying to take out all the people for the background. You can eq the bass frequencies really high and sort of make the bass stand out, or adjust the mids to get at the guitar, but it's going to be very difficult to isolate the guitar. Also how on earth is there an effects pedal that can do this, your talking about isolating guitar out of a song with drums, bass, guitar, and vocals, maybe other instruments. How is a pedal gonna do anything?