Self-assembled monolayers (SAMs) enable significant changes in the surface energy and/or specific interactions of surfaces, which are desirable for microelectromechanical systems (MEMS), superhydrophobic coatings, sensors, and other applications. However, SAMs often exhibit poor durability and rapid degradation upon mechanical, thermal, or moisture exposure. The chemical and orientational changes in SAMs due to mechanical and thermal degradation were investigated using near-edge X-ray absorption fine structure (NEXAFS) and the water contact angle. SAMs were based on unfluorinated or fluorinated linear hydrocarbons that form highly oriented and densely packed structures on silicon substrates. Complex chemical and orientational changes were observed via NEXAFS following degradation. Under heating in a dry, oxygen-rich environment, unfluorinated SAMs tended to cleave at C-C bonds on the main chain; below 250 degrees C, CH(3) groups were sequentially cleaved toward the surface, whereas above 250 degrees C, remaining hydrocarbon groups were converted to a graphitic coating dominated by C=C bonds. Under similar conditions, fluorinated SAMs began their chemical degradation at 350 degrees C and above, although the orientation decreased steadily from 150 to 300 degrees C; at and above 350 degrees C, the preferential removal of F occurred and the SAM was slowly converted to a graphitic layer. By contrast, under vacuum the fluorinated molecules were very thermally stable, showing good stability up to 550 degrees C; when degradation occurred, entire molecules were removed. Mechanical degradation followed two routes; both unfluorinated and fluorinated SAMs that were mechanically rubbed with smooth surfaces exhibited severe chemical degradation of the molecules, leading to an amorphous and poorly defined layer with C=C, C-C, C-H, and C-F bonds. Unfluorinated and fluorinated surfaces that were mechanically rubbed in the presence of free silicon particulates showed the rapid and complete destruction of both the molecular orientation and the protective SAM layer, even for short exposure periods. The resulting NEXAFS spectra were very similar to those produced by heating to 550 degrees C, suggesting that the friction created by granular particles may lead to extreme local heating.