A method is proposed involving obtaining data regarding an expected focus offset during a patterning process due to topography of a region of a substrate surface. A modification of, e.g., a transmission or reflection of a region of a patterning device associated with the region of the substrate surface is determined based on the data. Using the patterning device modified according the determined modification during the patterning process mitigates an impact of the substrate topography on a parameter of the patterning process.