Parameters important to the self-assembly of 3-(aminopropyl)triethoxysilane (APTES) on chemically grown silicon oxide (SiO2) to form an aminopropyl silane (APS) film have been investigated using in situ infrared (IR) absorption spectroscopy. Preannealing to similar to 70 degrees C produces significant improvements in the quality of the film: the APS film is denser, and the Si-O-Si bonds between the molecules and the SiO2 surface are more structured and ordered with only a limited number of remaining unreacted ethoxy groups. In contrast, post-annealing the functionalized SiO2 samples after room temperature reaction with APTES (i.e., ex situ annealing) does not lead to any spectral change, suggesting that post-annealing has no strong effect on the horizontal polymerization as suggested earlier. Both IR and ellipsometry data show that the higher the solution temperature, the denser and thinner the APS layer is for a given immersion time. Finally, the APS layer obtained by preannealing the solution at 70 degrees C exhibits a better stability in deionized water than the APS layer prepared at room temperature.