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. By scanning target structures in the same or similar direction to the feature placement, blurring at the edges of interest is avoided and a line-to-line or edge-to-edge offset between pattern elements is less susceptible to error from blurring at scanned edges of interest. For example, at least two linear pattern elements corresponding to at least two sample layers may be scanned along or parallel to the direction of feature placement (i.e., along or parallel to long edges of the pattern elements).