The roughness at the surface of individual pentacene terraces on naturally oxidized silicon wafers was investigated with scanning force microscopy as function of film thickness (one to five layers) and sample exposure to ambient air. For pristine samples, the root-mean-square roughness on individual (001) pentacene terraces was 0.18 nm and varied by less than 0.02 nm between monolayer terraces and terraces in the fifth layer. Storing samples in air and ambient light led to a substantial increase of the roughness, which for terraces up to the third layer became 0.24 nm after four weeks. For fourth layer terraces, the roughness increased less, and terraces in the fifth layer exhibited no significant roughness increase. We explain the roughness increase by photo-oxidation of pentacene, particularly strong within the first layer, which is supported by the appearance of grain boundary widening with storage time. The observation that layers beyond the third one from the substrate are less affected by photo-oxidation (smaller terrace roughness) is likely due to better structural perfection in layers farther from the substrate, which reduces the effective cross-section of molecules for oxidation. These results indicate that native silicon oxide does not allow for the immediate formation of structurally perfect pentacene films in the range of one to three layers, which will reduce charge carrier mobility in pentacene thin film transistors. Thicker pentacene layers can protect underlying layers against oxidation. (C) 2010 Elsevier B.V. All rights reserved.