A thin film battery manufacturing method comprises annealing a battery substrate to a temperature at which organic materials are burned off the battery substrate to clean the battery substrate. The battery substrate comprises a thickness of less than about 100 microns. After annealing, a plurality of thin films are formed on the annealed battery substrate, the thin films comprising at least one electrolyte between a pair of electrodes, and the thin films adapted to generate or store an electrical charge. The thin films can also be annealed to remove defects in the thin films.