Embodiments described herein relate to substrate processing methods. More specifically, embodiments of the disclosure provide for an MRAM back end of the line integration process which utilizes a zero mark for improved patterning alignment. In one embodiment, the method includes fabricating a substrate having at least a bottom contact and a via extending from the bottom contact in a first region and etching a zero mark in the substrate in a second region apart from the first region. The method also includes depositing a touch layer over the substrate in the first region and the second region, depositing a memory stack over the touch layer in the first region and the second region, and depositing a hardmask over the memory stack layer in the first region and the second region.