Cost, durability, and reliability are the major issues hindering the commercialization of polymer electrolyte membrane fuel cells. Electrolyte membranes present in the fuel cell fails under chemical, thermal, and mechanical influences, which, in turn, results in the overall fuel cell failure. In the present work, 2D studies are performed to understand the effect of manufacturing processing conditions and materials on the quality of the high-temperature membranes. Multiphase computational fluid dynamics models are used for solving the flow behavior of a shear-thinning non-Newtonian fluid. The viscosity and velocities were found to have a profound effect on the membrane structure.