In this paper, the assembly and stability of locally spotted spherical nanoparticles ontovarious substrates are studied. Arrays of silicon-based microcantilevers, combined with anautomated three-stage spotter, are used to deposit picolitre droplets containing 300 nmdiameter polyethylene glycol and 150 nm diameter amino conjugated silica nanospheres ontosilicon, allylamine and acrylic acid surfaces. Matrices of colloid spots ranging from 10 to100 µm in diameter have been successfully patterned. SEM characterizations of thenanoparticles’ geometry and spatial distribution within the spots were carried out,showing the colloid aggregation at the droplet’s rim and the selective stabilityof the printed patterns. The expected substrate functionalization was assessedby XPS characterizations of the nanoparticles’ surfaces. Finally, polyethyleneglycol–SiO2 nanoparticle conjugates were used as masks during a selective reactive ion etching of thesilicon substrate, and silicon nanopillars have been obtained. This work opens uppossibilities of high spatial resolution nanopatterning with nanoparticle conjugates.