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This paper has developed a new method of micro patterned electroplating that enables the fabrication of micrometer scale magnetic structures on glass substrates. In contrast to other methods, the process as developed here leaves the surrounding substrate area untouched: that is there is no seed layer present except underneath the magnetic structures. Patterned cobalt layers of thicknesses up to 8 μm were fabricated exhibiting high saturation (1.5 T) and low coercive force. These layers have been used to create micrometer scale magnetic poles (magnetic tweezers) for biological and biophysical applications, where a clean untouched glass substrate in the sample area is most important. The technique, however, can be used in any situation where a residual seed layer on the surrounding area is unwanted, and afterwards removal of this seed layer is difficult or impossible.