The domain structure in thin films of an immiscible polystyrene/poly(methyl methacrylate) (PS/PMMA) blend was studied after spin-casting from a common solvent. Atomic force microscopy (AFM) combined with selective dissolution was used to obtain three-dimensional information on the domain morphology in thin films. Three different common solvents and three different substrate surfaces were studied. Distinct differences in the thin film domain structure and surface topography are observed depending on the substrate surface energy and the solubility of the two polymers in the three solvents. The topographic modulation can be explained by a different rate of solvent evaporation during spincoating for the two phases. The normal and lateral organization of the phase-separated domains is governed by a complex interplay between preferential aggregation of one phase at the substrate and phase segregation in the film. Additionally, some of the results suggest that a dewetting process may be involved in the domain formation. The structures obtained after spin-casting are far from thermodynamic equilibrium. The equilibration of the films during annealing depends strongly on the phase morphology, and long-lived metastable configurations are found.