The growth of an opal-like polymer photonic crystal (PhC) on deeply etched silicon wafers is reported. It is shown that 10 μm deep trenches, as narrow as 10 μm can be uniformly filled by self-assembly of microspheres, in a close-packed face-centered-cubic lattice. These observations are confirmed by optical reflectance measurements in the visible range, in agreement with theoretical calculations of the photonic band gap. A slight fluctuation of the lattice parameter is noticed in the case of the narrowest channels. The possibility to detach the PhC from the substrate is also demonstrated. The potential of this approach for building complex PhC-based complex architectures is discussed.