We introduce a model for thin films of multicomponent fluids that includes lateral and vertical phase separation, preferential component attraction at both surfaces, and surface roughening. We apply our model to thin films of binary polymer blends, and use simulations of different surface-blend interaction regimes to investigate pattern formation. We demonstrate that surface roughening couples to phase separation. For films undergoing lateral phase separation via a transient wetting layer, this results in distinct stages of roughening as the film evolves between different phase equilibria. DOI: 10.1103/PhysRevLett.113.218301 PACS numbers: 82.35.Lr, 64.75.St, 64.75.Va, 68.55.am Semiconducting polymer devices, such as photovoltaic films, can gain performance enhancements from phase separated morphologies. Since polymer films are prone to surface roughening, understanding how phase separation couples to dewetting is particularly important. This interplay was highlighted by Walheim et al. for spin-cast polymer films [1] and has been repeatedly observed, e.g., phase separation in symmetrically surface-segregating films [2-5], lateral phase separation via a transient wetting layer [6,7], and phase separation proceeding from the surface as the solvent evaporates [8]. Pattern formation in polymer blend thin films, in which surface roughening shadows the phase separated morphology, is incredibly common [9,10]. Theoretical results suggest that, generally, the coupling of phase separation and height variation makes films less stable [11] and can trigger instabilities [12,13].A variety of models for multicomponent deformable fluid films have been investigated. The "Clarke model" (name introduced here) utilized nonequilibrium thermodynamics based upon a free energy functional, demonstrating that phase separation generally couples to dewetting [12]. A model based on the Navier-Stokes Cahn-Hilliard equations in the lubrication approximation showed that concentration gradients can create a roughened pattern that mirrors the underlying phase separation [14]. However, the film composition has no vertical dependence in these models, so a meaningful preferential surface attraction of blend components cannot be included. Two-layer models exist, including models with immiscible fluid layers [15,16] and layers with a diffuse boundary for films with no preferential surface attraction [17]. However, a general vertical composition dependence, which could allow vertical phase separation to occur during a simulation, is typically not included [9], though such a case has been studied with regards to stability but not simulated [18]. An exception is a model of surface roughening of polymer blend films, although this model is not based upon a dewetting film [19].This Letter presents a model formulation of a binary blend thin film which, by way of including a general vertical dependence of composition, can be utilized for a full time simulation of coupled dewetting and phase separation, including (i) both lateral and vertical phase separat...