A method of determining an optimal operational parameter setting of a metrology system is described. Free-form substrate shape measurements are performed. A model is applied, transforming the measured warp to modeled warp scaling values. Substrates are clamped to a chuck, causing substrate deformation. Alignment marks of the substrates are measured using an alignment system with four alignment measurement colors. Scaling values thus obtained are corrected with the modeled warp scaling values to determine corrected scaling values. An optimal alignment measurement color is determined, based on the corrected scaling values. Optionally, scaling values are selected that were measured using the optimal alignment measurement color and a substrate grid is determined using the selected scaling values. A substrate may be exposed using the determined substrate grid to correct exposure of the substrate.