Embodiments of the disclosure provide methods and apparatus for fabricating magnetic tunnel junction (MTJ) structures on a substrate for MRAM applications. In one embodiment, a method for forming a magnetic tunnel junction (MTJ) device structure includes performing a patterning process by an ion beam etching process in a processing chamber to pattern a film stack disposed on a substrate, wherein the film stack comprises a reference layer, a tunneling barrier layer and a free layer disposed on the tunneling barrier, and determining an end point for the patterning process.