I feel a screw protruding slightly from the bottom of a plate inserted to repair a trimalleolar fracture. Is it possible to have that one screw removed or must all the hardware come out?

Sometimes. It could just be the one screw removed but it would all depend on the plate configuration. See your orthopedist.
Yes. Most likely you can have one screw removed without jeopardizing the stability of the plate or the repair.