Embodiments of the disclosure provide methods and apparatus for fabricating magnetic tunnel junction (MTJ) structures on a substrate in for spin-transfer-torque magnetoresistive random access memory (STT-MRAM) applications. In one embodiment, the method includes patterning a film stack having a tunneling barrier layer disposed between a magnetic reference layer and a magnetic storage layer disposed on a substrate to remove a portion of the film stack from the substrate until an upper surface of the substrate is exposed, forming a sidewall passivation layer on sidewalls of the patterned film stack and subsequently performing a thermal annealing process to the film stack.