We report various stages of self-organized, sub-micron, surface directed patterns in a thin polystyrene (PS) layer (thickness ~20nm) sandwiched between a silicon substrate and a cross-linked elastomeric layer(polydimethylsiloxane; PDMS, thickness ~20nm). The PS layer was swelled and dewetted by exposure to saturated cyclo-hexane vapor, owing to the lateral diffusion of the solvent vapors starting from the bilayer edges. Morphological evolution of the self-organized surface patterns was recorded both on the elastic PDMS surface and on visco-elastic PDMS-PS interface. The instability patterns could be aligned by placing a micro-stamp (pitch 1500 nm) in conformal contact on the surface of the PDMS-PS bilayer. The presence of the external micro-stamp on the PDMS layer directed the stress-driven patterns formed on the buried PDMS-PS interface, inducing anisotropic and regular surface pattern very similar to that on the master stamp. Such a control was found to be possible only when the order of magnitude of the characteristic length scale of the instability was similar to that of external stamp pattern. AFM scans of the top elastic PDMS surface and optical micrographs confirmed this contact-less transfer of master pattern uniformly over a larger area (cm2). The anisotropic surface pattern thus formed on the PDMS and PDMS-PS interfaces was employed to explore the subsequent stages of development of the self-organized sub micron structures formed by continued exposure of the bilayer to solvent vapors. Subsequent stages of self organization in this system refers to alignment of sub-micron structures in the grooves (width ~750 nm) of initial pattern followed by their morphological and topographical evolution in terms of shape, size, separation and aerial density. It was confirmed by the AFM scans of the top PDMS layer that the formation of such self-organized sub-micron structures occurs in the PS layer only. However the self organized micro structures along the tracks of the initial pattern were clearly visible in the optical micrographs of the bilayer samples. Thus the transparent nature of PDMS made it possible to record and investigate the later stages of self-organization where the self organized surface patterning occurred at the buried visco-elastic PDMS-PS interface only. The morphological evolution of these structures was studied in detail by characterizing their shape, size, average separation, number density along the grooves and aerial density. It is noteworthy that the periodicity of the corrugated pattern formed in the first stage of self organization remains undisturbed in the subsequent stages. Choice of materials, thickness of polymer films and certain key changes in experimental protocol made it possible to record different stages of self organization on a convenient time scale (~15 hrs).