A self-aligned via of a MRAM cell that connects a memory element including a top electrode, a memory element stack having a plurality of layers, and a bottom electrode to a bit line running over array of the memory elements. The self-aligned via also serves as a hard mask for memory element etching. The hard mask material has high selectivity in the etching ambient to maintain enough remaining thickness. It is also selectively removed during dual damascene process to form a self-aligned via hole. In one embodiment, Aluminum oxide or Magnesium oxide is adapted as the hard mask.