The morphology and composition of self organized manganese (Mn)-rich nanocolumns embedded in germanium (Ge) thin films were characterized at the atomic scale and in three dimensions with high resolution transmission electron microscopy and atom probe tomography. Experiments revealed Mn-enriched nano-columns of 3 nm in diameter with various morphologies. Their Mn-content was found smaller than that of the expected equilibrium phases and chemical fluctuations along the growth axis were additionally observed. By contrast, less than 0.05% of Mn was measured in the Ge-matrix. These results were correlated to the magnetic properties and allowed understanding the magnetic behavior of the nanocolumns.