Microstencil lithography, a resistless, single-step direct vacuum patterning method, is one of promising methods for metal micropattern definition on polymer substrates that are not suitable for conventional photolithography. We propose to apply microstencil lithography to fabricate microelectrodes on flat and pre-structured polymer substrates which form parts of microfluidic systems with incorporated microelectrodes. However, microstencil lithography is accompanied by two main issues when considered as a low-cost, reproducible alternative to standard photolithography on polymer substrates: clogging and blurring. The clogging of stencil apertures induced by metal evaporation was checked in detail, and it was determined that approximately 50 % of the thickness of the evaporated metals was deposited at the side walls of the stencil apertures. The influence of gap presence on the deposited structures was also analyzed experimentally, and we quantified the pattern blurring.