A method for manufacturing a magnetic memory element structure using a Ru hard mask and a post pillar thermal annealing process. A Ru hard mask is formed over a plurality of memory element layers and an ion milling is performed to transfer the image of the Ru hard mask onto the underlying memory element layers. A high-angle ion milling an be performed to remove any redeposited material from the sides of the memory element layers, and a non-magnetic, dielectric material can be deposited. A thermal annealing process can then be performed to repair any damage caused by the previously performed ion milling processes.