A photomask blank substrate is made by polishing a starting substrate to a specific flatness in a principal surface region on a top surface of the substrate so as to form a polished intermediate product, then additionally polishing the intermediate product. Substrates made in this way exhibit a good surface flatness at the time of wafer exposure. When a photomask fabricated from a blank obtained from such a substrate is held on the mask stage of a wafer exposure system with a vacuum chuck, the substrate surface undergoes minimal warping, enabling exposure patterns of small geometry to be written onto wafers to good position and linewidth accuracies.