We present an experimental and theoretical analysis of the formation of nanovoids within Si microcrystals epitaxially grown on Si patterned substrates. The growth conditions leading to the nucleation of nanovoids have been highlighted, and the roles played by the deposition rate, substrate temperature, and substrate pattern geometry are identified. By combining various scanning and transmission electron microscopy techniques, it has been possible to link the appearance pits of a few hundred nanometer width at the microcrystal surface with the formation of nanovoids within the crystal volume. A phase-field model, including surface diffusion and the flux of incoming material with shadowing effects, reproduces the qualitative features of the nanovoid formation thereby opening new perspectives for the bottom-up fabrication of 3D semiconductors microstructures.