A method for measuring overlay between an interest level and a reference level of a wafer includes applying a magnetic field to a wafer, detecting at least one residual magnetic field emitted from at least one registration marker of a first set of registration markers within the wafer, responsive to the detected one or more residual magnetic fields, determining a location of the at least one registration marker of the first set registration markers, determining a location of at least one registration marker of a second set of registration markers, and responsive to the respective determined locations of the at least one registration marker of the first set of registration markers and the at least one registration marker of the second set of registration markers, calculating a positional offset between an interest level of the wafer and a reference level of the wafer. Related methods and systems are also disclosed.