We investigated the early and intermediate stages of the guided dewetting of polystyrene (PS) thin films on chemically patterned silicon, achieved by micro-contact printing of non-wettable self-assembling monolayers of an alkylsilane. Two different types of ordered patterns could be achieved depending on the annealing temperature and time. Study of the dynamics of hole growth revealed a deviation of the growth profile from the trend on homogeneous substrates, attributed to the pinning of the PS rims on the borders of the hydrophobic regions. The ordered patterns produced could be useful in applications that require spatially localized features of controlled surface chemistry, such as studies in proteomics, single cell studies, and biosensors.