A method of processing substrates, in one example microelectronic workpieces, is disclosed that includes forming a multi-layer metal hard mask (MHM) layer in which at least one lower layer of the multi-layer MHM is comprised of ruthenium (Ru). The Ru MHM layer may be an atomic layer deposition (ALD) Ru MHM layer formed over one or more underlying layers on a substrate. The ALD Ru MHM layer may be etched to provide a patterned ALD Ru MHM layer, and then the one or more underlying layers may be etched using, at least in part, the patterned ALD Ru MHM layer as a mask to protect portion of the one or more underlying layers. In one embodiment, at least one of the underlying layers is a hard mask layer.