Helical swimming is adopted by microswimming robots since it is an efficient mechanism and commonly observed among microorganisms swimming at low Reynolds numbers. However, manufacturing of micro-helices made of sub-micron magnetic thin layers is neither straightforward nor well-established, advanced materials and methods are necessary to obtain such structures as reported in the literature. In this paper, a topological patterning method utilizing basic microfabrication methods is presented for the self-assembly of magnetic micro-helices made of a sandwiched nickel thin film (50–150 nm) between two silicon nitride layers. Strain mismatch between the thin films and the geometric anisotropy introduced by the slanted patterns on the top nitride layer result in self-rolled-up helical microribbons. Moreover, inspired by the actual release process during the wet-etching of the microribbon from the substrate, moving boundary conditions are incorporated in a numerical model to simulate the self-rolling of trilayer ribbons. The simulation results are compared and validated by experimental data within 7% error for all cases, including the geometries that do not result in a helical shape. The swimming performance of the magnetized micro-helix is demonstrated inside a capillary glass tube experimentally and cross-validated with a numerical model.