Superior properties for complex photonic integrated circuits can be obtained by materials other than silicon but compatible with established silicon electronics, e.g., germanium. In this work, we demonstrate the integration with silicon of fully relaxed germanium-on-insulator nanolayers enabled by micro-holes patterning. The heterosystems are fabricated thanks to the combination of epitaxy, electron beam lithography, and condensation. High resolution transmission electron microscopy and geometrical phase analyses show that for holes patterning with periodicities lower than 1 µm, the germanium nanolayers are fully relaxed and free of extended defects, while having numerous defects for larger periodicities and unpatterned settings. The experimental results are discussed with the aid of calculations of the stress for coherent epitaxial silicon–germanium layer with finite size effects and phase-field simulations accounting for the morphological evolution of the germanium crystals. The fabrication method presented here enables the growth of thick monocrystalline germanium-on-insulator layers, with great potential for optoelectronic devices with tunable dimensions and high quality. Also, these systems are suitable for high-speed germanium-on-Si photodetectors with enhanced quantum efficiency resulting from light manipulation by the array of holes. This innovative system, which is expected to operate at the visible and near-infrared range of wavelengths, has huge potential for cutting-edge applications where photodetectors and bipolar transistors are integrated into the same wafer e.g. facial recognition and LIDAR.