How do i make what looks like warts (but the bumps don't hurt) go away?

Probably no need: Warts generally are not painful except when they occur at a spot sensitive to pressure, rubbing, etc (e.g. plantar warts, on the soles of the feet). Common warts in children almost always clear up on their own within a few months and usually it's best to just leave them alone. But if they increase in number or are bothersome (to him, not you), take him to the pediatrician for treatment advice.