Under defined growth conditions ferromagnetic hexagonal Mn5Ge3 precipitates are formed in cubic Ge1-xMnx epilayers. To study the topotaxial relationship of these nanomagnets we perform x-ray diffraction experiments in coplanar as well as in grazing incidence geometries at synchrotron sources. Additionally, to the well defined topotaxial relation derived for buried nanomagnets deep within the Ge layer, we found an additional class of Mn5Ge3 precipitates very close to the surface, with larger inclusion diameter and several different crystallographic orientations with respect to the buried ones.