Abstract: Presented are systems for manufacturing membrane electrode assemblies for fuel cells, control logic for operating such systems, methods for making such MEAs, and fuel cell systems employing such MEAs. A method of manufacturing a membrane electrode assembly (MEA) for a fuel cell system includes receiving a standalone membrane (SAM) with a semipermeable proton-exchange membrane having opposing first and second faces and a backing layer attached to the first face. A SAM may be characterized by a lack of cathode and anode electrodes upon receipt of the membrane. The second face of the SAM is placed across a vacuum plate; the vacuum plate applies a predefined vacuum pressure to the SAM. While vacuum pressure is being applied to the SAM by the vacuum plate, the backing layer is removed from the SAM. A subgasket is then attached to the first face of the SAM after the backing layer is removed.