We report a combined atomic force microscopy/x-ray diffraction study of the growth and dewetting of the organic molecule di-indenoperylene (DIP) on SiO2 surfaces that have been functionalized with an amino-terminated self-assembled monolayer of 3-aminopropyltriethoxysilane [APS, (CH3CH2O)(3)Si(CH2)(3)NH2]. We disclose a transition of DIP thin films from two-dimensional to three-dimensional growth at 80 degrees C, which is associated with a change in the surface morphology of APS during the annealing of the substrates. This growth scenario gives rise to the formation of micron sized DIP single crystals, which could be potentially interesting for future application in electronic devices.