Silicon-Germanium in a hexagonal crystal-structure is a candidate material for a direct band-gap group IV semiconductor that can be integrated into the CMOS process. It has recently been synthesized as a crystalline shell grown epitaxial around a nanowire core of hexagonal Gallium-Phosphide. In order to study the optical properties of this newly generated material and evaluate its potential for building optical devices it is necessary to grow defect and impurity free hexagonal Silicon-Germanium. Impurity detection and mapping in nano-structures is however challenging as most bulk and thin film characterization methods cannot be used. Here we show that Atom Probe Tomography can be used to map the impurities in hexagonal shells of Silicon-Germanium and Silicon. This will allow to optimize growth of hexagonal Silicon-Germanium nanocrystals towards impurity free, optically active crystals.