Mask shops typically use carbon to repair any clear defects identified on a mask, irrespective of the type of mask. However, carbon can have different characteristics than the original patterning material on the mask. Therefore, a mask that is repaired using carbon may not optically perform as if it were defect-free. An automated method of repairing a clear defect on an attenuated phase shifting mask (PSM) provides an optimized plug size/shape. In this method, a repair solution to the clear defect can be simulated, thereby allowing the repair decision for an attenuated PSM to be advantageously made at the same time that inspection is done and before actual repair. Simulation can include performing model-based OPC on the repair solution.