In the experimental study of thin polymer films, a two-stage sample preparation scheme is commonly used: the polymer film is cast first onto mica, and then the film is transferred to another substrate via a water bath. We present evidence of polymer chain conformational or compositional changes arising from the annealing history of the film on mica. Flow dynamics and rim morphology of dewetting holes in monodisperse polystyrene films on hydrophobized silicon wafers are examined using optical and atomic force microscopy. A significant difference in flow dynamics and rim morphology of holes is observed. The difference depends on whether the interface of the film that was previously in contact with mica remains the interface that touches the hydrophobized substrate from which the film dewets. In this case the difference is consistent with a reduced slip boundary condition, and the reduction depends on pre-annealing to be observed. Furthermore, the slip length disparity is sensitive to the molecular weight distribution of the dewetting films. The disparity of boundary conditions is attributed to long-lasting compositional or conformational arrangements arising from surface segregation and/or surface ordering of chains or their segments. (C) 2015 Elsevier Ltd. All rights reserved.