A large-size glass substrate, from which a photomask substrate is formed, is prepared by processing a large-size glass substrate stock by (1) a flattening removal quantity based on height data of the substrate stock in the vertical attitude plus a deformation-corrective removal quantity. The deformation-corrective removal quantity is calculated from (2) a deflection of the substrate stock by its own weight in the horizontal attitude, (3) a deformation of the photomask substrate caused by chucking in an exposure apparatus, and (4) an accuracy distortion of a platen for supporting a mother glass.