For the wafer-scale fabrication of diamond devices, the growth of diamond substrates by heteroepitaxial chemical vapor deposition is the most promising option currently available. However, the transfer of growth and also structuring processes from small homoepitaxial to larger heteroepitaxial samples is not straightforward and requires adaptation. In this study, we present an approach for the fabrication of functional microstructures including pyramids and mesas as well as more complex structures with hollow centers. The associated methods were previously demonstrated by homoepitaxial growth and are now evaluated on heteroepitaxially grown diamond films. After optimizing the growth procedures to ensure a sufficient quality of the bare diamond substrates, precursor structures for overgrowth were fabricated by e-beam lithography and plasma etching. In the overgrowth of nanopillars, a truncated pyramidal shape was achieved. The characterization with scanning electron microscopy revealed the growth of higher-index facets. Nevertheless, photoluminescence spectroscopy reveals localized doping on the sides of the microstructures. In addition, optically detected magnetic resonance reaches a contrast of 6% of one preferred nitrogen vacancy orientation per facet and a transverse relaxation time T2∗ of 96 ns.