Microfluidic systems with incorporated microelectrodes are adopted in a variety of applications in life sciences. However, most of micro-electro-fluidic devices are fabricated based on silicon and silicon related materials micromachining processes, which are still expensive for disposable or semi-disposable sensing devices. Plastics and other polymer materials are advantageous to be used as substrates of microfluidic systems in order to realize a low-cost production process of devices, since these materials can be easily structured by e.g. hot-embossing, injection molding or thermal forming with excellent reproducibility. However, the lithographical process of microelectrode fabrication on plastic substrates is one of the critical issues, because many of these materials cannot withstand organic solvents which are unavoidable during conventional photolithography processes. Microstencil lithography, i.e., local deposition of micrometer scale metal patterns through small shadow masks, is a promising method for metal micropattern definition on plastic substrates that are not feasible for solvent-based photoresist technology. Since microstencil lithography is a resistless, single-step direct vacuum patterning method, it enables us to simplify the device fabrication process as well. Thus, we propose to apply microstencil lithography to fabricate microelectrodes onto plastic substrates as part of a low-cost production process of microfluidic devices. However, microstencil lithography is faced with several possible drawbacks. Therefore, we focused on two specific issues accompanying microstencil lithography, which are expected to affect on micro electro fluidic device fabrication process when considered as low-cost, reproducible alternative to standard lithography on plastic substrates: clogging and blurring. One of the main limitations of microstencil lithography is that the method is associated with gradual aperture clogging. To suppress the clogging phenomenon, coating stencils with self-assembled monolayers (SAM) is highly helpful, by which the useful life time of stencils can be extended. But in this study, we traced the clogging of micro-apertures without SAM coating by an observation of the stencil apertures and deposited microstructures after each evaporation step in order to asses the basic feasibility of microstencil lithography. From the series of observation, it was determined that approximately 50 % of the thickness of the evaporated metals (Ti, Cu) was deposited at the side walls of the stencil apertures, i. e., when 200 nm of Ti was evaporated through the microstencil, the thickness of deposited Ti at the side wall of the aperture was 0.1 um. Similar values were observed when Cu was used as a deposited material. The progress of clogging is clearly visible in an SEM image, in which the corresponding microstencil aperture was observed from the side having faced the substrate during the evaporation. These results suggest that the microstencils can be used repeatedly even without a cleaning treatment when the device specifications allow some micrometer tolerance of the electrode size. The other drawback of stencil lithography is related to the gap presence between the stencil and the substrate. We will also present quantitative values of gap induced clogging and discuss the blurring mechanism of deposited structures based on a simplified geometrical model.