A selective electrothermal magnetic annealing technique is introduced that provides programming capabilities for mechanical micro-resonators. In the proposed approach, the magnetic properties of resonators can be locally tuned in a post-fabrication batch-compatible process step. A prototype is implemented in a standard microfabrication process, where resonating ferromagnetic elements are suspended on top of a polysilicon resistive heater. The ferromagnetic elements consist of electroplated Nickel (Ni) with minor Iron (Fe) impurities. The electro-thermo-mechanical heating phenomenon is simulated for design purposes. The magnetization of micro-resonators with and without magnetic annealing is measured. The resulting magnetic property enhancement is illustrated by hysteresis (M-H) loop variations.