Thin films, formed by polymer blends spun-cast from a blend/solvent solution onto a rigid substrate, are used in many practical applications (e.g. photoresist layers, dielectric coatings). Film preparation process is often accompanied by phase decomposition (PD) during the rapid evaporation of the solvent. PD is reflected in undulations formed on an air/film interface. We have studied the topography of surface undulations and the phase domain morphology in thin film blends of polystyrene (PS) and polyisoprene (PI) using atomic force microscopy combined with selective dissolution of blend components. Gold covered with self-assembled monolayers [HS(CH2)15COOH]y[HS(CH2)15CH3]1−y (SAMy) was used as a substrate. For films of PS and PI (50% by mass) cast from toluene, the PS-rich domains protrude high above the PI-rich matrix forming concave or convex islands for hydrophobic (SAM0)- or hydrophilic (SAM1)-support, respectively. Different substrates (e.g. SAM0.5 and Si with a native oxide layer), solvents (CCl4, chloroform) and PS mass fractions were used to evaluate the extent of this novel effect.