Diamond with engineered nanostructures such as holes or nanopillars networks provides an useful platform for optical or photonic devices in which light can be extracted or confined. Moreover improvement of the structural properties of the material is expected after overgrowth of specific nanopatterns that can act as dislocation filters or stress release layers. Usually nanostructures are realized using multiple lithographic procedures that are costly and time consuming to implement. In this work another approach is used in which nanopillars of different diameters (200, 100 nm) are fabricated on nanocrystalline diamond (NCD) films and single crystal diamond (SCD), using self‐assembled silica nanospheres as shadow mask for inductively coupled plasma‐reactive ion etching (ICP‐RIE). The particles assembly and etching steps are optimized in order to obtain a uniform distribution of pillars having a high aspect ratio. Following the patterning of SCD the authors performed an overgrowth of a diamond film by CVD on the nanostructures in order to study their evolution and the final crystal quality. It is found that impurities such as SiV preferentially incorporate into the nanopillars. These structures could find useful applications to harness light extraction or control the dislocation propagation in CVD diamond.