Sectional views of thin films of symmetric polystyrene/polyisoprene (PS/PI) blends spin-cast from toluene (C6H5CH3) onto CH3- and COOH-terminated self-assembled monolayers (CH3−SAM and COOH−SAM) show concave- (sharp-edged) and convex-shaped (round) protrusions, respectively, while other morphology features are identical. A 3-dimensional phase domain arrangement was determined with spectroscopic techniques (profiling and mapping mode of dynamic secondary ion mass spectrometry, dSIMS, and X-ray photoelectron spectroscopy). Surface topography was examined with atomic force microscopy and monitored, during the dSIMS analysis, with secondary electrons. In addition, solvent evaporation from PS, PI, and PS/PI layers cast on CH3−SAM and COOH−SAM was determined. The collected data were used to put forward a model of morphology formation and to elucidate the role of evaporation speed dependent on substrate chemistry in this process, demonstrated here for the first time.