The present invention provides a method for producing a thin film lithium battery, comprising applying a cathode current collector, a cathode material, an anode current collector, and an electrolyte layer separating the cathode material from the anode current collector to a substrate, wherein at least one of the layers contains lithiated compounds that is patterned at least in part by a photolithography operation comprising removal of a photoresist material from the layer containing lithiated compounds by a process including a wet chemical treatment. Additionally, a method and apparatus for making lithium batteries by providing a first sheet that includes a substrate having a cathode material, an anode material, and a LiPON barrier/electrolyte layer separating the cathode material from the anode material; and removing a subset of first material to separate a plurality of cells from the first sheet. In some embodiments, the method further includes depositing second material on the sheet to cover the plurality of cells; and removing a subset of second material to separate a plurality of cells from the first sheet.