Disclosed is a method of determining calibrated reference exposure and measure grids for referencing position of a substrate stage in a lithographic system. The method comprises obtaining calibration data relating to one or more calibration substrates; and determining an exposure grid for an exposure side of the lithographic system from said calibration data and a measure grid for a measure side of the lithographic system from said calibration data. The exposure grid and said measure grid are decomposed so as to remove a calibration substrate dependent component from said exposure grid and from said measure grid to obtain a substrate independent exposure grid and substrate independent measure grid.