One method disclosed herein includes forming a layer of insulating material above a semiconductor substrate, forming a hard mask layer comprised of a metal-containing material above the layer of insulating material, forming a blanket protection layer on the hard mask layer, forming a masking layer above the protection layer, performing at least one etching process on the masking layer to form a patterned masking layer having an opening that stops on and exposes a portion of the blanket protection layer, confirming that the patterned masking layer is properly positioned relative to at least one underlying structure or layer and, after confirming that the patterned masking layer is properly positioned, performing at least one etching process through the patterned masking layer to pattern at least the blanket protection layer.