Systems and methods for forming embedded memory in a processing unit. The methods include: depositing a dielectric layer on a metal landing pad of a logic circuit of a processing unit; opening vias in the dielectric layer; filling in the vias; performing chemical mechanical polishing (CMP); depositing an adhesion and topography planarization (ATP) layer; etching away portions of the ATP layer; filling in with inter layer dielectric (ILD) materials; performing CMP; depositing a MTJ film layer; patterning and etching away portions of the MTJ film layer; filling in with dielectric materials; performing CMP; and forming a bit line on the top layer. The methods may also include annealing in a forming gas during different steps of the above processed to reduce the high stress from the making of multi-metal layers of the processing unit at high temperature. This may prevent wafer warpage and/or significant topography in the fabrication process.