In this article the authors present the use of nanomagnets as fine alignment features for structures assembled by folding nanopatterned membranes. The membranes are patterned with arrays of nanomagnets that passively align to other arrays. They analyze the scaling of the force between magnets and calculate the required structural compliance for the magnetic forces to actuate the membranes. A model of the alignment system that captures the magnetic forces and the membrane dynamics has been developed. They show that an external magnetic field provides magnetic saturation of the nanomagnets and aligns the membranes rotationally. The magnetic dipole approximation used in the model was confirmed experimentally by patterning cobalt and iron nanomagnets on silicon nitride cantilevers and actuating in an external magnetic field. Self-alignment between the two arrays of cobalt nanomagnets was achieved confirming the magnetic alignment principle. (c) 2006 American Vacuum Society.