We report the structural, electronic and magnetic investigation using extended X-ray absorption fine structure spectroscopy (EXAFS), photoelectron microscopy, spin-resolved photoemission and magneto-optical Kerr effect on the properties of MnGe systems obtained by molecular beam epitaxy deposition of manganese on Ge(001) wafers annealed on temperatures between 50 and 450 C. Magnetic ordering can be achieved when the substrate temperature is higher than 250 C, when the manganese tends to diffuse into the Ge matrix and segregate in MnGe-like compounds, as proved by EXAFS. High spatial resolution photoelectron spectroscopy reveals Mn inhomogeneities in the 5-10 m range, even though Mn is found mostly in the same chemical state all over the surface.