In polymer electrolyte membrane (PEM) fuel cells and electrolyzes, attaining and maintaining high membrane conductivity and durability is crucial for performance and efficiency. The use of low equivalent weight (EW) perfluorinated ionomers is one of the few options available to improve membrane conductivity. However, excessive dimensional changes of low EW ionomers upon application of wet/dry or freeze/thaw cycles yield catastrophic losses in membrane integrity. Incorporation of ionomers within porous, dimensionally-stable perforated polymer electrolyte membrane substrates provides improved PEM performance and longevity. The present invention provides novel methods using micromolds to fabricate the perforated polymer electrolyte membrane substrates. These novel methods using micromolds create uniform and well-defined pore structures. In addition, these novel methods using micromolds described herein may be used in batch or continuous processing.