We propose an integrated top-down and bottom-up approach to single-step nanofabrication of complex nanostructures made of different materials. The process, termed lithographically controlled etching (LCE), starts with a drop of an etching solution cast on the surface to be patterned. By placing a polymeric mold on the substrate, the stamp protrusions come into contact with the surface, thus protecting it, whereas the surface beneath the mold recesses is exposed to a thin layer of etching solution, allowing the surface to be etched. By dispersing nanoparticles into the etching solution, these can be deposited and self-organize in the recesses on the substrate as these are excavated. We demonstrate here the fabrication of complex structures and nanowires 30 nm wide. Moreover, by exploiting capillary forces, it is possible to deposit nanoparticles at precise positions with respect to optically addressable microstructures, thus realizing a multiscale functional pattern.