The main physical difference is usually the diameter of the hole. A normal plated-thru-hole (PTH) is usually made to have a wire or a lead of a component soldered into it, or maybe to have a fastener pass through. The inner diameter of the hole, after plating, is sized such as to receive the wire, pin or fastener with sufficient clearance. A via is a special kind of PTH that's not intended to receive anything. It's purpose is only to provide a conductive path from one PCB layer to another. Thus, its hole diameter is usually much smaller than a normal PTH.