This research disclosure relates to an algorithm and method for wafer alignment. Especially, it is related to a wafer alignment algorithm that does not require training wafers to set-up a recipe. The algorithm may be used for determining (relative) positions of alignment marks on a substrate (e.g.. a semiconductor wafer) loaded, for example, in a lithographic apparatus or a metrology system. The proposed algorithm uses all colors/photons such that the variance of an estimated wafer deformation is minimized (minimum variance unbiased estimation). This minimization of the estimation variance (due to measurement noise), also minimizes the estimation bias (of the estimated wafeT deformation). The primary subject matter is the color weighting of the measured positions (as a function of wavelength) by the signal strengths {i.e., the average diffraction order intensity or wafer quality (WQ)), with the first objective of doing so, to increase/maximize the robustness for process variations and with the second objective to increase/maximize the robustness for measurement noise.
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