Developing optoelectronic devices, biological or chemical sensors, displays, and other devices based on nanoparticles (NPs) requires designing tailored NP assemblies on solid substrates, and often with a given surface positioning. In our study, we discuss a new soft-lithographic method for patterning an organic layer, which is capable of binding gold nanoparticles (AuNPs) to the surface. AuNPs with a citrate shell were 17 nm in diameter and prepared by the Turkevich protocol. Our method is based on controlling the binding capability of (3-aminopropyl)trimethoxysilane (APTES)-coated surface by deactivating the -NH2 terminal groups of APTES under the action of UV-generated ozone in air. We show that partial and complete deactivation can be achieved depending on the atmosphere and exposure time. Using a shadow mask during irradiation, we furthermore show that our method can be applied for creating micron-scale arrays of NPs on APTES-coated substrates with a spatial resolution down to similar to 1.5 mu m, currently limited by the properties of the mask.