The phase separation kinetics of ultrathin deuterated poly(styrene)/poly(butadiene) polymer blend films spun cast onto striped self-assembled monolayer (SAM) substrates is studied by atomic force microscopy (AFM). Fourier transform analysis of the AFM topographic data at various stages of the film pattern development reveals the presence of quantized surface deformation modes. These modes are excited by the phase separation process when the scale of phase separation becomes commensurate with the period of the striped surface pattern. Thus, higher frequency modes become excited at early stages of phase separation, and these excitations decay with time as the phase separation pattern further coarsens. The film ultimately self-organizes into a periodic structure in which the fundamental mode has the largest amplitude. The influence of film thickness on the film morphology in this late stage is also investigated. A decrease in the film thickness leads to surface patterns that match those of the SAM substrates with increasing resolution. However, these film patterns break up into droplet arrays along the SAM stripes if the films are made too thin. This phenomenon is attributed to a capillary wave instability.