Deposition of size-selected copper and silver nanoparticles (NPs) on polymers using cluster beam technique is studied. It is shown that ratio of particle embedment in the film can be controlled by simple thermal annealing. Combining electron beam lithography, cluster beam deposition, and heat treatment allows to form specific patterns (arrays) of metal NPs on polymer films. Plasticity and flexibility of polymer host and specific properties added by coinage metal NPs open a way for different applications of such composite materials, in particular, for the formation of plasmonic structures with required configurations which can be applied for wave-guiding, resonators, in sensor technologies, and surface enhanced Raman scattering.