Embodiments of the invention are described that use a thin metallic hard mask, which can be a bi-layer film, to increase the incident IBE angle for MTJ sidewall cleaning without losing the process margin for the subsequent interconnection process. The patterned metallic hard mask pads also serve as the top electrode for the MTJ cells. Using a thin metallic hard mask is possible when the hard mask material acts as a CMP stopper without substantial loss of thickness. In the first embodiment, the single layer hard mask is preferably ruthenium. In the second embodiment, the lower layer of the bi-layer hard mask is preferably ruthenium. The wafer is preferably rotated during the IBE process for uniform etching. A capping layer under the hard mask is preferably used as the etch stopper during hard mask etch process in order not to damage or etch through the upper magnetic layer.