A photomask is manufactured by a method including providing a substrate having a surface on which a predetermined pattern is to be formed, positioning the substrate in an exposure tool so as to obtain an amount of deformation of the surface due to an external force imposed on the substrate, calculating a target profile of the surface, based on the amount of deformation and a target flatness of the surface, and processing the surface of the substrate so as to make the surface substantially flat when the substrate is positioned in the exposure tool.