The present disclosure relates to a method of monitoring wafer topography. A position and orientation of a plurality first alignment shapes disposed on a surface of a wafer are measured. Wafer topography as a function of wafer position is modeled by subjecting the wafer to an alignment which simultaneously minimizes misalignment between the wafer and a patterning apparatus and maximizes a focus of radiation on the surface. A non-correctable error is determined as a difference between the modeled wafer topography and a measured wafer topography. A maximum non-correctable error per field is determined for a wafer, and a mean variation in the maximum non-correctable error across each field within each wafer of a lot is determined, both within a layer and across layers. These values are then verified against a set of statistical process control rules to determine if they are within a specification limit of the manufacturing process.