Elastic recoil detection (ERD) analysis of GeOx thin films was carried out to understand the mechanism of phase separation. Stoichiometry of the film was monitored on-line at various fluences of 100MeV Au ions. Although significant electronic sputtering of GeOx film was observed but the stoichiometry remained almost constant up to a fluence of 3×1012ions/cm2. Structural modifications of the films after irradiation was studied by offline glancing angle X-ray diffraction (GAXRD), which showed the presence of Ge crystallites in the films. The results indicate that the phase separation does not occur because of preferential sputtering of oxygen but may occur as a result of rearrangement of Ge and O atoms within the films. The activation for rearrangement is provided by ion impact.