Abstract: Substrate masking apparatus includes a platen assembly to support a substrate for processing, a mask having an aperture, a retaining mechanism to retain the mask in a masking position, and a positioning mechanism to change the relative positions of the mask and the substrate so that different areas of the substrate are exposed through the aperture in the mask. The apparatus may further include a mask loading mechanism to transfer the mask to and between the masking position and a non-masking position. The processing may include ion implantation of the substrate with different implant parameter values in different areas. In other embodiments, an area of the substrate to be processed is selectable by a mask, a shutter or a beam modifier in front of the substrate.