Silicon and Germanium naturally occur in a cubic crystal structure and have an indirect bandgap1 making them unsuitable materials for light emission. When synthesized in a hexagonal crystal structure Germanium and Silicon-Germanium are however predicted to have a direct bandgap2 which makes these crystal phases candidate materials for integrating optical functionality into silicon based CMOS. We have recently demonstrated the synthesis of hexagonal silicon3 using Gallium-phosphide nanowires with a hexagonal crystal lattice4as a virtual substrate. Based on this approach we have succeeded in growing hexagonal Germanium and Silicon-Germanium both as shells around and branches on Gallium-phosphide nanowires. We are now aiming to grow optically active hexagonal Germanium and Silicon-Germanium with a direct bandgap. However, in order to create efficient light sources, we will have to suppress non-radiative recombination channels in the material and hence grow defect and impurity free hexagonal Germanium and Silicon-Germanium. This makes it necessary to measure the defect and impurity level inside the hexagonal shells and branches. Unfortunately, the size and the geometry of the structures make these measurements challenging as typical bulk characterization methods like Secondary Ion Mass Spectroscopy or X-Ray Diffraction are not applicable. Here we will show how we use Transmission Electron Microscopy (TEM) and Atom Probe Tomography (APT) to monitor the crystal structure, crystal defect density, impurity level, interface roughness and matrix concentration in this complex material system. TEM allows us to investigate the defect density and defect formation during the growth of the hexagonal lattices making it possible to work towards the growth of defect free structures. APT allows us to create three-dimensional images of the elemental distribution inside the structures and hence makes it possible to supervise the impurity level, interface roughness and matrix concentration in the structures. Combining the two methods thus enables us to optimize the growth parameters, minimizing both the defect and the impurity density. [1] M. Cardona et al. Phys Rev., 142:530, 1966. [2] C.Raffy et al. Phys. Rev. B, 66:075201, 2002. [3] H. I. T. Hauge et al. Nano Lett., 15(9):5855, 2015. [4] S. Assali et al. Nano Lett., 13(4):1559, 2013. Figure 1: Defects and impurities in a hexagonal Si shell (a-d) and hexagonal Ge branches (e,f) grown on GaP nanowires. Side-view imaging with TEM (a,c,f) enables us to identify defects. In combination with cross-section TEM images (b) we can confirm the epitaxial growth of Si on the hexagonal GaP lattice. APT analyses of the Si shells (d) and the Ge branches (e) allow us to map impurity atoms in the hexagonal crystals and reveal the diffusion of Ga and P into the Si and the Ge respectively. Figure 1