In a simulation step, based on information of a main surface shape of a transparent substrate and shape information of a mask stage of an exposure apparatus and using a deflection differential equation taking into account a twist deformation, height information at a plurality of measurement points is obtained by simulating a state where the transparent substrate is set in the exposure apparatus. Based on the height information obtained through the simulation, a flatness of the transparent substrate when it is set in the exposure apparatus is calculated in a flatness calculation step. Then, by judging in a selection step whether or not the calculated flatness satisfies a specification, the transparent substrate whose flatness satisfies the specification is used as a substrate for a mask blank.