Pathways to fabricate self-organized nanostructures have been identified exploiting the instabilities of ultrathin (<100 nm) polystyrene (PS) film on the polydimethylsiloxane (PDMS) substrates loaded with discrete and closely packed gold nanoparticles (AuNPs). The AuNPs were deposited on the PDMS substrates by chemical treatment, and the size and periodicity of the AuNPs were varied before coating the PS films. The study unveils that the physicochemical heterogeneity created by the AuNPs on the PDMS surface could guide the hole-formation, influence the average spacing between the holes formed at the initial dewetting stage, and affects the spacing and periodicity of the droplets formed at the end of the dewetting phase. The size and spacing of the holes and the droplets could be tuned by varying the nanoparticle loading on the PDMS substrate. Interestingly, as compared to the dewetting of PS films on the homogeneous PDMS surfaces, the AuNP guided dewetted patterns show ten-fold miniaturization, leading to the formation of the micro-holes and nanodroplets. The spacing between the droplets could also see a ten-fold reduction resulting in high-density random patterns on the PDMS substrate. Further, the use of a physicochemical substrate with varying density of physicochemical heterogeneities could impose a long-range order to the dewetted patterns to develop a gradient surface. The reported results can be of significance in the fabrication of high-density nanostructures exploiting the self-organized instabilities of thin polymers films.