Metallic nanoparticles from the gas phase were deposited onto silicon substrates, which are pre-coated with multilayers of amphiphilic phospholipids. If the lateral molecular mobility of these lipid molecules is sufficiently high, a lipid monolayer is formed around individual nanoparticles. At the same time, the molecular mobility of the multilayer allows for self-assembly of the particles in regular two-dimensional arrangements. The inter-particle distance and the degree of order within the particle arrangements is found to depend strongly on the phase state of the lipid multilayer during the particle deposition as well as during the post-deposition annealing step. The implementation of a homogeneous magnetic field perpendicular to the multilayer results in hexagonal particle patterns of high symmetry. Solid supported multilayers of various phospholipids were prepared by spin coating. Here, the use of silicon wafers as substrates often results in lipid multilayers, which already show defects immediately after the preparation step. Various experiments with different phospholipids show that the formation of these surface defects is primarily determined by the chemical structure of the lipid head group. Using substrates that were chemically modified with a polymerized layer of the phospholipid PC-Diyne, homogeneous multilayers of various phospholipids could be prepared.