We present the results of a study of the morphology of phase separation in a thin him blend of polystyrene (PS) and polyisoprene (PI) in a common solvent of toluene. The blend is quenched by rapid solvent evaporation using a spincoating technique rather than a temperature quench The mass fraction of polystyrene is varied to determine the effect of the substrate on thin film phase separation morphology. We compare the phase separation morphology for very thin films of the PS/PI blend cast onto three different substrates : Si(001) with a native oxide layer (Si-SiOx), Si(001) etched in hydrofluoric acid (SI-H), and a Au/Pd alloy sputtered onto Si(001). We observe large differences between the morphologies of 1000 Angstrom thick blend films on the Si-SiOx and Si-H substrates as the mass fraction is varied due to the difference in the wetting properties of PS on the two substrates. Smaller differences are observed between the films on the Si-SiOx and Au/Pd substrates only for film thicknesses h < 600 Angstrom.