Electron energy loss spectroscopy maps using a transmission electron microscope were used to investigate with nanometer spatial resolution the Mn distribution of a MnxGe1-x ion implanted alloy (x similar or equal to 4%). Mn is fully diluted in the Ge matrix in a subsurface implanted layer, showing concentration inhomogeneities at the nm scale. In the deep implanted layers the presence of Mn rich clusters-either amorphous or in the Mn5Ge3 phase-is directly evidenced. Scanning Tunneling Microscopy/Spectroscopy directly shows that the Mn5Ge3 clusters are metallic, while those smaller and amorphous are semiconducting with 0.45 +/- 0.05 eV band gap. The Ge matrix with Mn dilution is semiconducting with 0.60 +/- 0.05 eV gap. Electronic structure results are compared with ab-initio calculations. (c) 2006 Elsevier B.V. All rights reserved.