Methods for MTJ patterning for a MTJ device are provided. For example, a method includes (a) providing an MTJ device comprising a substrate comprising a plurality of bottom electrodes, a MTJ layer disposed on the substrate, and a plurality of pillars disposed on the MTJ layer and over the plurality of bottom electrodes, wherein the plurality of pillars comprise a metal layer and a hard mask layer disposed on the metal layer, (b) conducting a first ion beam etching of the MTJ device; (c) rotating the MTJ device by 90 degrees in a clockwise or a counter clockwise direction about an axis perpendicular to a top surface of the MTJ device from a starting position; (d) conducting a second ion beam etching of the MTJ device; and (e) repeating steps (c) and (d).