You just have to grind it down where it fits snugly in the stock again, remember that the recoil pad is the 'structure' in the back end of the stock and without that structure it is weak and will break. Easy enough right? Well, not really. You have to pay attention to the screw holes in the stock, as you shorten up the stock and start fitting the pad it is easy to get the two out of sync. Take material off the pad evenly and check often for screw hole alignment.
I use a semi-smoothing rasp, a double cut bastard file works nicely too.