Nanofabrication of buried structures with dimensions below 5 nm and with controlled 3D-positioning at the nanoscale was attempted to open new routes to future nanodevices where single nanostructures could be systematically interfaced. A typical example is ultralow-energy ion beam synthesis where already the depth positioning of embedded arrays of silicon nanocrystals can be finely controlled with nanometric precision. In this study, we investigated for the first time the control of the in-plane organization of the nanocrystals using a legitimate patterning option for microelectronic industries, self-assembled block-copolymer. The compatibility with the ultralow-energy ion beam synthesis process of polymeric nanoporous films used as mask was demonstrated together with the capability to control in 3D the organization of Si nanocrystals. The resulting nano-organization consists in a hexagonal array of 20 nm wide …