Contact angle measurements and scanning force microscopy (SFM) have been used to study the morphology of self-assembled monolayers of octadecyltrichlorosilane (OTS) and undecyltrichlorosilane (UTS) on silicon oxide surfaces as a function of annealing temperature. Characterization of the monolayers before annealing indicates that the as-formed monolayers cover the substrate fully and have thicknesses of 2.9 and 1.5 nm, respectively, with the average surface having a roughness of approximately 0.3 nm. Water contact angle results and SFM roughness analysis showed that UTS monolayers annealed for 2 h at temperatures over 125 degrees C exhibited permanent changes in monolayer structure. Experimental data indicated a higher transition temperature for permanent structural changes for the OTS monolayers. Water contact angle measurements indicated a transition centered at 125 degrees C, hexadecane contact angle measurements indicated a transition around 130 degrees C, and SFM indicated a transition centered at 155 degrees C for OTS monolayers. We have observed that contact angle measurements can be sensitive to surface structure on an angstrom length scale. These results observed after 2 h are not equilibrium results, as evidenced by the further development in the monolayer after an anneal for 5 h. Thermodynamic considerations support the earlier (lower temperature) changes observed for UTS than for OTS monolayers. The observed transition is likely the result of hydrolysis of the organic molecules by water molecules existing at the monolayer-substrate interface.