We study the patterns spontaneously formed by bilayer polymer films upon annealing. Specifically, polystyrene (PS) films were spin-cast on topographically patterned poly(methyl methacrylate) (PMMA) substrates and subsequently annealed at temperatures above the glass transition temperature of both polymers. The influence of the molecular weight and the volume of PS on the morphological evolution of the corrugated liquid–liquid interface was examined. When the PS formed isolated stripes both on the mesas and within the trenches of the PMMA pattern, capillary instability was observed for these nonaxisymmetric PS threads. The kinetics of the capillary breakup depended on the thread-to-matrix viscosity ratio, and was dictated by the more viscous component. In contrast, the characteristic wavelength of the breakup only slightly depended on some viscosity ratio, and reached a minimum at the viscosity ratio around 1. When the PS was thick enough to form a continuous layer, the instability of the film further depended on the molecular weight of the PS. For a molecular weight of 13 kg/mol, the PS dewetted from PMMA via a random nucleation and growth mechanism. However, for a molecular weight of 2000 kg/mol, localized nucleation on top of the PMMA mesas led to a mesh-like PS morphology, which eventually broke up due to capillary instability. Therefore, by controlling the molecular weight and the spin-cast volume of the top layer, the kinetics of morphological evolution and the resulting patterns can be controlled.