Stability of nanoparticle filled multi-polymeric systems have attracted significant interest due to the fact that addition of such particles drastically changes the properties of the polymers and have huge potential in the field of optoelectronic devices, nanocoatings. With this work, we present here a fundamental study on morphological stability on addition of fullerene NP in poly(styrene) (PS)/ poly(methylmethaacrylate) (PMMA) blend thin films. PS and PMMA being immiscible polymer blends at room temperature laterally phase segregates leading to formation of meso scale surface structures. Atomic Force Microscope images of as coated PS-PMMA blend reveals that on increasing the concentration of NP, the lateral phase segregated domains reduces. Moreover, beyond a critical concentration, the phase segregation is completely arrested leading to a flat film. By ellipsometric studies, thickness of the polymer blend with nanoparticle before and after selective phase removal hinted vertical phase separation instead of a typical lateral phase separation. We can qualitatively infer that the nanoparticles while spin coating, migrates towards the polymer–polymer interfaces and impart stability to the interface, thereby arresting the lateral phase segregation process during the latter stages of spin coating. This interfacial stability led to a vertical phase segregation of the PS and PMMA forming a polymer–polymer bilayer. This technique can be used to coat ultra-thin multifunctional coatings without the need of additional coating processes. While the effect of addition of NP is well known for imparting stability to single layer of polymer thin film, for the case of polymer bilayer with NP, a reduction in dewetted length scale of top layer is observed between specific ranges of concentration and the dynamics of the instability becomes sluggish. Apart from stability, this provided an additional parameter to impart miniaturization in dewetted morphology.