Multilayers of various phospholipids on silicon substrates are used to induce spontaneous embedding of nanoparticles deposited from the gas phase. The resulting nanoparticle arrangement on the substrate surface is characterized using atomic force and scanning electron microscopy. In the intermediate phase and the liquid crystalline phase of the lipid, a monolayer is formed around individual nanoparticles which leads to an increase in interparticle distances. At the same time, the molecular mobility of the multilayers allows for self-assembly of the particles in regular two-dimensional arrangements. (C) 2004 American Institute of Physics.