Microtransfer molding (µTM) and microcontact printing (µCP) techniques were demonstrated for the preparation of platinum based catalysts in hexagonally arranged patterns to achieve cathode catalyst layers (CCLs) with microscale patterned features. These soft lithographic techniques, previously demonstrated for use in the preparation of patterned thin films, were adopted to produce patterned CCLs for proton exchange membrane fuel cells (or PEMFCs) with features having a thickness up to 20 µm. The resulting CCLs contained precise microscopic patterns that could be tuned for improving the performance of PEMFCs. It was demonstrated that CCLs containing arrays of microscale, cylindrical holes as prepared by µTM exhibited an improvement in their water management characteristics within PEMFCs when compared to CCLs prepared from continuous catalyst films. Upon further tuning of the CCL transfer procedures for µCP of CCLs, the formation of isolated microscale, disc-like features were demonstrated to have twice the mass activity of that observed for PEMFCs containing CCLs with uniform thin catalyst films. These methods to prepare patterned CCLs are compatible with current manufacturing techniques and could be easily adapted to incorporate other catalyst materials for further improvements in PEMFC performance. The soft lithography techniques used herein could also be scaled up to meet the industrial demand of large volume manufacturing.