Vacuum condition influence on the thermally induced self-organization of thin film of 6 monolayers (ML) of Au on atomically flat Ge(001) surface was studied by Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM) techniques. Metallic islands, up to 100 nm in size, were found on samples annealed at Ultra High Vacuum (UHV) conditions just after Au deposition. Annealing of air exposed samples resulted in the formation of big islands, up to 400 nm in size together with small ones, 10 nm in size. In opposite, samples annealed at 3 mbar of H2O vapour pressure were found to have surface etched into the inverted pyramid pits formed around Au clusters. The size of the etched pits is proportional to the size of Au clusters.