The present invention describe a substrate handling system that exerts no or controllable external forces to hold substrates, does not contact front or back of the substrates, has minimum contact with side edge area of the substrate, can hold one or two substrate to each position, can be positioned in any orientation, and can be easily handled by human or robots. In the case that no deposition materials is desirable on the edge or sides of substrate, a self-aligned mask that can be attached to the substrate carrier is presented.