The integration of high performance RE-TM (NdFeB and SmCo) hard magnetic films into Micro-Electro-Mechanical-Systems (MEMS) requires their patterning at the micron scale.In this paper we report on the applicability of standard micro-fabrication steps (film deposition onto topographically patterned substrates, wet etching and planarization) to the patterning of 5 µm thick RE-TM films. While NdFeB comprehensively fills micron scaled trenches in patterned substrates, SmCo deposits are characterized by poor filling of the trench corners, which poses a problem for further processing by planarization. The magnetic hysteresis loops of both the NdFeB and SmCo patterned films are comparable to those of non-patterned films prepared under the same deposition/annealing conditions. A micron-scaled multipole magnetic field pattern is directly produced by the unidirectional magnetization of the patterned films. NdFeB and SmCo show similar behavior when wet etched in an amorphous state: etch rates of approximately 1.25µm/minute and vertical side walls which may be attributed to a large lateral over-etch of typically 20 µm. ChemicalMechanical Planarization (CMP) produced material removal rates of 0.5-3µm/min for amorphous NdFeB. Ar ion etching of such films followed by the deposition of a Ta layer prior to film crystallization prevented degradation in magnetic properties compared to nonpatterned films.