Gold nanoparticles were immobilized on silicon dioxide (SiO2) surfaces by embedding them in a layer of octadecylsiloxane (ODS) and also in SiO2 layers created by deposition and oxidation of ODS layers. The ODS and the SiO2 layers form selectively around the nanoparticles. Analysis of the particles after several deposition/oxidation cycles showed a decrease in measured height in accordance with the number of deposited layers. Following one embedding cycle, the nanoparticles could not be moved with the tip of a scanning force microscope operated in dynamic mode, whereas they moved in a controlled fashion prior to the deposition of any layer. Depositing a second set of particles onto an ODS layer in contact with the substrate allowed us to construct a two-particle column by placing one particle directly on top of another one.