Meso scale structures obtained due to phase segregation of an immiscible polymer blends has attracted significant interest over the years as these surfaces can potentially be used in a wide variety of applications such as anti–reflection coatings in organic solar cells, as templates in tissue engineering, as templates for selective deposition, as multifunctional substrates for combinatorial studies and many more. Such polymer blends when spin coated on a flat substrate results into variety of random structures which largely depends on the composition of the two polymers, the film thickness as well as the nature of the substrate. With this work we investigate polystyrene (PS) / poly(methylmethaacrylate) (PMMA) blend thin films of various concentrations and compositions spin casted on flat as well as on different topographically patterned substrates. Myriad of nanostructures were obtained on varying parameters such as molecular weight of the polymers, the surface energy of flat and patterned substrates and nature of the topographic confinement. Three broad regimes of the phase segregated morphology could be identified based on the concentration (Cn); Regime 1: Cn <0.5%, at which the solution spin dewets, resulting in isolated polymer droplets aligned along substrate grooves, Regime 2: at an intermediate Cn where isolated threads are formed with aligned phase segregated domains along each substrate groove, and finally in Regime 3:above a critical concentration (Cn*) which depends strongly on ratio of the blend composition, the overall morphology of the film transforms forms discontinuous to continuous. The physical confinement imposed by the topographical patterns enabled ordering of these domains which are otherwise random and also significant miniaturization of the domain size was also achieved. While the extent of ordering of the domains gradually diminishes with increase in film thickness (vis-à-vis Cn), the size of the domains remains much smaller.