The fundamental properties of hyperthermal atomic oxygen or atomic fluorine-exposed polyimide and polyethylene surfaces, based on the analytical results by X-ray photoelectron spectroscopy and contact angle measurements, are reported. It was observed that CF, CF2 or CF3 moieties were formed at the atomic-fluorine-exposed polymer surfaces depending on the fluence, whereas carbonyl and carboxyl groups were formed at the atomic oxygen-exposed polymer surfaces. Advancing contact angles of water can be controlled from 60 to 150 degrees by varying the atomic oxygen or atomic fluorine fluence. It was also demonstrated that a selected area on the target surface could be processed with this method using a fine metal mask. The behavior of a water droplet on polymer surfaces could be controlled by the spatially resolved surface modification using hyperthermal atomic beams.