An application of scanning Auger microscopy with ion etching technique and effective compensation of thermal drift of the surface analyzed area is proposed for direct local study of composition distribution in the bulk of single nanoislands. For GexSi1 − x-nanoislands obtained by MBE of Ge on Si-substrate gigantic interdiffusion mixing takes place both in the open and capped nanostructures. Lateral distributions of the elemental composition as well as concentration-depth profiles were recorded. 3D distribution of the elemental composition in the d-cluster bulk was obtained using the interpolation approach by lateral composition distributions in its several cross sections and concentration-depth profile. It was shown that there is a germanium core in the nanoislands of both nanostructure types, which even penetrates the substrate. In studied nanostructures maximal Ge content in the nanoislands may reach about 40 at.%.