A method for aligning a wafer image with a reference image, comprising: searching for a targeted reference position on the wafer image for aligning the wafer image with the reference image; and in response to a determination that the targeted reference position does not exist: defining a current lock position and an area that encloses the current lock position on the wafer image; computing an alignment score of the current lock position; comparing the alignment score of the current lock position with stored alignment scores of positions previously selected in relation to aligning the wafer image with the reference image; and aligning the wafer image with the reference image based on the comparison.