Fuel cells have gained renewed interest for applications in portable power since the energy is stored in a separate reservoir of fuel rather than as an integral part of the power source, as is the case with batteries. While miniaturized fuel cells have been demonstrated for the low power regime (1-20 Watts), numerous issues still must be resolved prior to deployment for applications as a replacement for batteries. As traditional fuel cell designs are scaled down in both power output and physical footprint, several issues impact the operation, efficiency, and overall performance of the fuel cell system. These issues include fuel storage, fuel delivery, system startup, peak power requirements, cell stacking, and thermal management. The combination of thin-film deposition and micro-machining materials offers potential advantages with respect to stack size and weight, flow field and manifold structures, fuel storage, and thermal management. The micro-fabrication technologies that enable material and fuel flexibility through a modular fuel cell platform will be described along with experimental results from both solid oxide and proton exchange membrane, thin-film fuel cells.