The present disclosure provides a method of cleaning a semiconductor wafer during a process of fabricating a semiconductor device. The method includes loading a semiconductor wafer into a wafer handling system. The method includes removing contaminant particles from an edge region of the wafer from the back side, wherein alignment marks are located in the edge region. The method includes collecting the removed contaminant particles and discarding the collected contaminant particles out of the wafer handling system. The disclosure also provides an apparatus for fabricating a semiconductor device. The apparatus includes a wafer cleaning device that is operable to clean a predetermined region of the wafer on the back surface thereof. The predetermined region of the wafer at least partially overlaps with one or more alignment marks.