We investigate the transfer of a chemical pattern on a substrate into a symmetric diblock copolymer thin film of poly(styrene-2-vinylpyridine) (PS-PVP). The substrates have patterns of self-assembled monolayers (SAMs) produced by microcontact printing H3C-terminated (H3C-) SAM stripes alternating with HO-terminated (HO-) SAM stripes. The PS-PVP lamellae over the H3C-SAM have a defect structure that attracts excess PS-PVP that would normally form islands on a uniform HO-SAM stripe. We seek to understand the process that limits our ability to accommodate all excess polymers on top of the H3C-SAM. In the early stages of annealing, waves of thickness develop from the H3C/HO-SAM boundary and propagate into the film over the HO-SAM. For very short annealing times, the wavelength λ of these thickness waves is constant at any given time for all grating periodicities. Large amplitude patterns develop when λ = 2d/(2n - 1), where d is the width of the HO-SAM stripe and n is an integer ≥ 1. Such patterns suggest constructive interference of the thickness waves and indeed much lower amplitudes over the HO-SAM stripes are observed when λ = d/n (destructive interference). This behavior seems close to that seen for surface-directed spinodal decomposition waves in thin films of binary polymer mixtures. We achieve more complete transfer of excess copolymers from the HO-SAM stripe to the H3C-SAM ones if the film is preordered under a confining layer that does not permit the formation of surface features.