Poly(styrene-b-isoprene-b-styrene) (SIS) block copolymer ordering in thin films was studied using two selective substrates as carbon and silicon. Atomic force microscopy (AFM) and contact angle measurements were employed to examine the affinities between domains and surrounding interfaces. The surface morphology was examined by AFM using different amplitude ratios. Results showed polyisoprene (PI) domain layer formation in the outermost film layer. On the other hand, the layer close to substrate adopted different arrangements on silicon and carbon substrates. Topographical and phase images revealed that in both substrates with the thickest films, the interactions between substrate and block domains were not enough to induce surface ordering being the morphology independent of employed substrate. However, decreasing film thickness, SIS thin films displayed a variety of arrangements such as perforated lamellae and cylindrical morphologies. Depending on substrate, these morphologies were achieved in different film thicknesses. Finally, the thinnest film did not adjust to characteristic domain spacing commensurability and terraces formation was observed. (c) 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012