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The depth-dependent morphology of the microphase separation structure in thin block copolymer films is examined using non-destructive time-of-flight grazing-incidence small-angle neutron scattering. The structure of a cylinder-forming diblock copolymer, polystyrene(deuterated)-block-polyisoprene, in contact with either a low- or a high-energy substrate surface is investigated. A systematic identification of the components of the polymer film at different depths is achieved by utilizing the material characteristic Yoneda peak. For the polymer film attached to the low-surface-energy aminosilane-coated substrate, a morphology transition from lamellar at the substrate-polymer interface, via perforated lamellar in the film bulk, to an ill-defined structure at the polymer-air interface is observed. This phase transition along the film normal is due to the competition between the surface-induced morphological changes and the stable cylindrical bulk morphology of the diblock copolymer. In contrast, on the high-energy surface no pronounced ordering is found for the applied conditions.

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