A method is provided wherein a lithographic projection apparatus is used to print a series of test patterns on a test substrate to measure printed critical dimension as function of exposure dose setting and focus setting. A full-substrate analysis of measured critical dimension data is modeled by a response model of critical dimension. The response model includes an additive term which expresses a spatial variability of the response with respect to the surface of the test substrate. The method further includes fitting the model by fitting model parameters using measured critical dimension data, and controlling critical dimension using the fitted model.