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A rapid and simple method to fabricate tiny shadow-masks and their use in multi-layer surface patterning with in situ micromechanical alignment is presented. Instead of using silicon micromachining with through-wafer etching to define the thin membrane with etched apertures, we are using photoplastic SU-8-based resist as structural material of both membrane and support rim. Two layers, 5 and 150um thick, are structured by lithography and finally released from the surface. The free-standing SU-8 membranes have apertures ranging from 6 to 300um. They are placed and mechanically fixed to the surface, which needs to be patterned. Deposition by evaporation of Cr, Au, Al or other material through the membrane apertures results in an accurate 1:1 replication of the aperture pattern. In view of multi-layer patterning, we used in situ micromechanical alignment pins or jigs and achieved an overlay precision of <2um in both x- and y-directions. The reusable shadow-masks allows for a low-cost surface patterning technique without the need for photolithography related process steps. It allows unconventional surfaces to be patterned in a rapid and vacuum-clean way on arbitrary surfaces.