Microstencil lithography, i.e. local deposition of micrometer scale patterns through small shadow masks, is a promising method for metal micropattern definition on polymer substrates that cannot be structured using organic-solvent-based photoresist technology. We propose to apply microstencil lithography to fabricate microelectrodes on flat and 3D polymer substrates, such as PMMA or SU-8, which form parts of microfluidic systems with integrated microelectrodes. Microstencil lithography is accompanied by two main issues when considered for application as a low-cost, reproducible alternative to standard photolithography on polymer substrates. In this paper we assess in detail (i) the reduction of aperture size (clogging) after several metal evaporation steps and corresponding change of deposited pattern size and (ii) loss in the resolution (blurring) of the deposited microstructures when there is a several micrometers large gap between the stencil membrane and the substrate. The clogging of stencil apertures induced by titanium and copper evaporation was checked after each evaporation step, and it was determined that approximately 50% of the thickness of the evaporated metals was deposited on the side walls of the stencil apertures. The influence of a gap on the deposited structures was analyzed by using 18 um thick SU-8 spacers placed between the microstencil and the substrate. The presence of an 18 um gapmade the deposited structures notably blurred. The blurring mechanism of deposited structures is discussed based on a simplified geometrical model. The results obtained in this paper allow assessing the feasibility of using stencil-based lithography for unconventional surface patterning, which shows the limits of the proposed method, but also provides a guideline on a possible implementation for combined polymer-electrode microsystems, where standard photoresist technology fails.