We combine convective/capillary deposition and oxidation lithography by atomic force microscopy to direct the close-packed assembly of colloids on SiOx patterns fabricated on silicon substrates previously functionalized with a hydrophobic monolayer of octadecyltrimethoxysilane. The efficiency of this original generic method, which is well adapted to integrate colloids into silicon devices, is demonstrated for 100 nm colloidal latex nanoparticles and Escherichia coli bacteria in aqueous suspensions. A three-step mechanism involving convective flow and capillary forces appears to be responsible for these close-packed assemblies of colloids onto SiOx patterns.