A method includes a preparation step of preparing a transparent substrate having a precision-polished main surface, a surface shape information obtaining step of obtaining, as surface shape information, height information at a plurality of measurement points on the main surface of the transparent substrate that contacts a mask stage of an exposure apparatus, a simulation step of obtaining, based on the surface shape information and shape information of the mask stage, height information at the plurality of measurement points by simulating the state where the transparent substrate is set in the exposure apparatus, a flatness calculation step of calculating, based on the height information obtained through the simulation, a flatness of the transparent substrate when it is set in the exposure apparatus, a judging step of judging whether or not the calculated flatness satisfies a specification, and a thin film forming step of forming a thin film as serving as a mask pattern, on the main surface of the transparent substrate whose flatness satisfies the specification.