Selective deposition of diamond allows bottom-up growth of diamond nanostructures and nanoscale devices. However, it remains challenging to reduce the size of the patterns and to suppress parasitic spontaneous nucleation. We show here that thin layers of hydrtogenated amorphous silicon (down to 40 nm) efficiently suppress spontaneous nucleation of diamond. The suppression of diamond nucleation does not depend on the substrate materials below hydrogenated amorphous silicon (Si, SiO2, Pt, Ni). We attribute the suppressed diamond nucleation to surface disorder on atomic scale. By using a structured layer of hydrogenated amorphous silicon, highly selective growth of diamond micro-patterns with optically active SiV centers by low-temperature microwave plasma chemical vapor deposition is achieved.