Provided is a method for reducing phase defects on many different types of semiconductor mask blanks. The method includes receiving a semiconductor mask blank substrate, creating alignment marks on the surface of the substrate, performing an inspection of the surface of the substrate to locate a plurality of surface defects, and repairing the plurality of surface defects on the surface of the substrate. A semiconductor mask is also provided that includes a repaired substrate a multilayer stack comprising a plurality of molybdenum and silicon layers, a capping layer, an absorber layer, and in some instances a photoresist layer.