We have successfully demonstrated the patterning of Nafion membranes for multiple electrochemical applications using electron beam lithography and dry etching strategies. The fabricated structures include arrays of lines and circles with features as small as 300 nm. The fidelity of the patterned profiles showed a dependency on resist baking temperature, masking layer thickness, and feature size. The propagation of cracks on a patterned Nafion substrate due to relaxation of stresses caused by the vacuum and thermal processing cycles was mitigated by keeping electron beam resist baking temperatures between 70 and 80 degrees C or by increasing the thickness of the masking layer. The etching of Nafion was quantified for oxygen and trifluoromethane gas plasmas using germanium as etching mask. Nafion etch rate increased with power for both gases, but showed little dependence on temperature and pressure in the oxygen plasma. Aspect ratio dependent etching was also observed during fabrication, particularly for feature sizes less than 2 mu m. (C) 2011 The Electrochemical Society. [DOI: 10.1149/1.3615938] All rights reserved.