We report the first time observation of endotaxial growth during thermal treatment of size-selected nanoclusters on a patterned substrate, when we fabricate highly ordered and partially embedded 3D crystalline Cu nanostructure arrays of controlled size in Si-substrates. For this purpose, we combine low energy cluster deposition on the ripple-patterned substrate with controlled annealing. We have investigated, in detail, the effect of the substrate pattern on the deposited size-selected clusters upon heat treatment. At the annealing temperature of 400 °C, nanosized islands are found to be organized into regular arrays, following the alignment of the substrate pattern exactly. The formed islands are trapped at the specific sites of the substrate where surface curvature is maximum and concave. It is also observed that the size of the produced nanoislands (or particles) in the direction of the ripple wave vector, i.e., across the ripples, are in congruence with the ripple wavelength. All the formed islands are partially buried in the substrate and the growth inside the substrate exhibits endotaxial growth. Such an embedded size-controlled nanoscale system can be very promising as sinter-resistant heterogenous catalyst with strong potential in clean energy technology and industrial chemical synthesis.