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The phase separation of ultrathin polymer-blend films of polystyrene and polybutadiene on microcontact printed alkanethiol patterns with hydrophobic and hydrophilic end groups (− CH 3 and-COOH) is investigated by atomic force microscopy. Simulations suggest that the phase-separation morphology can be controlled through patterns that modulate the polymer-surface interaction, and this concept is verified experimentally. Length scale pattern control is found to be limited to a scale on the order of a few micrometers.