In this paper, we present an alternative approach for controlled nanoparticle organization on a solid substrate by applying dewetting patterns of charged polymer solutions as a templating system. Thin films of charged polymer solutions dewet a solid substrate to form complex dewetting patterns that depend on the polymer charge density. These patterns, ranging from polygonal networks to elongated structures that are stabilized by viscous forces during dewetting, serve as potential templates for two-dimensional nanoparticle organization on a solid substrate. Thus, while nanoparticles dried in pure water undergo self-assembly to form close-packed arrays, addition of charged polymer in the dispersion leads to the formation of open structures that are directed by the dewetting patterns of the polymer solution. In this study, we focus on the application of elongated structures resulting from dewetting of high-charge-density polymer solutions to align nanoparticles of silica and gold into long chains that are several micrometers in length. The particle ordering process is a two-step mechanism: an initial confinement of the nanoparticles in the dewetting structures and self-assembly of the particles within these structures upon further drying by lateral capillary attractions.