The process of local anodic oxidation of thin GeO films has been studied using an atomic force microscope. The electron-probe microanalysis showed that oxidized areas of a GeO film were germanium dioxide. The effect of the voltage pulse duration applied to the probe–substrate system and the atmospheric humidity on the height of the oxide structures has been studied. The kinetics of the local anodic oxidation (LAO) in a semi-contact mode obeys the Cabrera–Mott model for large times. The initial growth rate of the oxide (R0) significantly increases and the time of starting the oxidation (t0) decreases as the atmospheric humidity increases by 20%, which is related to an increase in the concentration of oxygen-containing ions at the surface of the oxidized GeO film. It was shown that nanostructures in thin GeO layers can be formed by the LAO method.