A method of aligning a wafer for semiconductor fabrication processes may include applying a magnetic field to a wafer, detecting one or more residual magnetic fields from one or more alignment markers within the wafer, responsive to the detected one or more residual magnetic fields, determining locations of the one or more alignment markers. The marker locations may be determined relative to an ideal grid, followed by determining a geometrical transformation model for aligning the wafer, and aligning the wafer responsive to the geometrical transformation model. Related methods and systems are also disclosed.