Abstract: In the manufacture of a substrate with a hydrophobic film used for a reference electrode of an ion sensor or the like, a hydrophobic film is formed on a substrate by irradiating a target consisting of a hydrophobic compound with a neutral atom beam and thereby effecting sputtering. The apparatus for effecting the sputtering comprises a target base disposed in a vacuum chamber, an atom beam gun for irradiating a target on the target base with a neutral beam, a substrate base and a shutter for controlling the passage of sputtered particles. A thin film that is manufactured is suitable for an ion sensor, such as an ISFET or the like or an enzyme sensor.