Metastable germanium monoxide (GeO) thin-insulating films have been investigated as a new promising material for oxidation scanning probe lithography. Amorphous GeO films were deposited onto cool Si substrates by thermal evaporation of GeO2<Ge-NCs> heterostructure in vacuum. Properties of GeO films were studied by means of IR spectroscopy, Raman spectroscopy, atomic force microscopy (AFM) and scanning electron microscopy. The nanopatterning of GeO films included three stages. First, AFM-induced local anodic oxidation of GeO layer was used to obtain GeO2 nanowires on Si substrate. After local anodic oxidation in high voltage (≥9 V) regime at 80% relative humidity, the cross-section profile of fabricated GeO2 protrusions contained anomalously high double peaks on a broad base (“two-story shape”). Then, thermal annealing was employed to decompose the GeO film into a GeO2 matrix and Ge nanoclusters. Third, after selective etching of GeO2 from the decomposed GeO film, trenches remained in the porous Ge layer instead of GeO2 nanowires. This may be a potentially useful lithographic approach for fabricating nanoscale structures.