In this paper, we study the localized deposition of ZnO micro and nanostructures deposited by non-reactive rf-magnetron sputtering through a stencil mask on ultra-thin (10 nm) SiO2 layers containing a single plane of silicon nanocrystals (NCs), synthetized by ultra-low energy ion implantation followed by thermal annealing. The localized ZnO-deposited areas are reproducing the exact stencil mask patterns. A resistivity of around 5×10−3 Ω cm is measured on ZnO layer. The as-deposited ZnO material is 97% transparent above the wavelength at 400 nm. ZnO nanostructures can thus be used as transparent electrodes for Si NCs embedded in the gate-oxide of MOS devices.