The present disclosure is directed to a method of performing SEM overlay metrology with scan direction substantially aligned with or parallel to feature placement or patterning of overlay target structures. A polishing liquid is supplied onto a polishing cloth attached on a turntable, and a semiconductor wafer to be polished is held by a top ring. A blurred pixel value for the output pixel is determined, where the blurred pixel value is based on the set of input pixels and associated labels from the boundary map that correspond to the set of input pixels.