The morphology of Ge overlayers with different thicknesses deposited on Si(001) at 560 degrees C, has been investigated with XPS peak shape analysis and AFM. From the peak shape analysis of the Ge 2p and the Si KLL lines we find island growth for all evaporations and no wetting layer. In the analysis, the structural parameters of the islands (coverage and height) are determined after each evaporation. The AFM images confirm island formation, and the magnitude of the structural parameters are in qualitative agreement with the XPS results. Additionally the amount of evaporated Ge is measured with RES and compared with the amount determined from the structural parameters of the islands. There is a systematic discrepancy which might be due to inaccuracy in the inelastic mean free path or to forward focusing effects.. Our study demonstrates that combining the complementary techniques, XPS peak shape analysis and AFM, gives a much more detailed picture of the surface nanostructure than with any of the techniques alone.