Metallization methods of polyimide by hyperthermal atomic oxygen and atomic fluorine beams were developed. An atomic fluorine beam with a translational energy of 6.2 eV modified the wettability of polyimide surfaces to provide an advancing water contact angle of 132 degrees. It was confirmed that in-air storage for 2 months did not alter the hydrophobic property created by the atomic fluorine beam. This stable beam-induced surface fluorination technique was then applied to site-selective electroless Cu plating on polyimide. It was demonstrated that changing the exposure sequence could create both positive- and negative-type plating processes.