Aggregation states of both stabilized (by organic ligands) and nonstabilized nanoparticles have been studied in solutions, on plain surfaces, and within the polyelectrolyte multilayer capsules to provide control over formation of aggregates and their uniformity. Adsorption of nanoparticles could be performed either simultaneously with polymers to achieve their uniform (nonclustered or nonaggregated) distribution or without polymers for obtaining nonuniform (clustered or aggregated) distribution. Nanoparticles were characterized; in synthesis of nanoparticles involving gold sulfide the reaction can be stopped at a desired time to control the location of the near-infrared absorption peak. The influence of the uniformity of the nanoparticles distribution on the temperature rise during laser light illumination is numerically calculated; it is shown that the temperature rise on the closely located nanoparticles is higher than on the stand-alone nanoparticles. Further applications of polymer controlled distribution of nanoparticles are anticipated in their self-assembly.