You have to find the rub before you can fix it. Most of the problems I've had ended up being tire or wheel problems. There can be one bit of tire that isn't seated right or has a slight bulge in it (replace the tire or seat it right). Or the wheel's a bit out of true, so the tire rubs when that part of the wheel comes around (re-true the wheel).

Only blame the fender if the rubbing doesn't occur once per wheel revolution.