We present experimental results showing that roughening in polymer blend films is driven by the underlying phase-separated morphology. To control morphology and stability, nanoparticles (NP) are added to poly(methyl methacrylate) (PMMA):poly(styrene-ran-acrylonitrile) (SAN) (50:50) films having a thickness of 550 nm. These PMMA:SAN films undergo symmetric wetting with PMMA layers at the surface and substrate and separate into PMMA-rich (A) and SAN-rich (B) coexisting phases. Three varieties of NP are investigated and either partition into A (NPA) or segregate weakly (NPw) or strongly (NPs) to the interface between A and B. Using scanning force microscopy, the surface roughness is monitored for films containing up to 20 wt % NP. Whereas rupture is observed in neat blends and blends with NPw or NPA, stable films are produced by the addition of only 2 wt % NPs. Although capillary fluctuations fail to predict roughening, a novel model based on the Laplace pressure produced by the internal morphology agrees with experimental results. For neat blends and blends with NPA, long wavelength fluctuations exhibit universal scaling with roughness, lambda(s) proportional to R-q(1/4). Although the origin of this coupling is unknown, we propose that spinodal decomposition during initial phase separation may trigger the long wavelength fluctuations. By identifying the driving force for roughening in nanocomposite films, we can better understand and control high-performance coatings containing incompatible components and functional inorganic additives.