If it is not enough where you notice it, you should be able to adjust is out. Tighten your barrel adjuster on the brakes until it just starts to rub. Then adjust it out. Tighten the barrel adjuster down a click adn adjust again. Do this until you are at a pretty tight tolerance. You will need to check for radial true also. That is checking to see if the rim is still round.
Hey, it's a MTB. It dosen't have to be perfect like a roadie.
Read some of the wheel truing info either here or on the parktools web site.