We have investigated the mechanism of UV photopatterning of binary alkanethiolate self-assembled monolayers (SAMs) adsorbed on Au(111) using time-of-flight secondary ion mass spectrometry. The SAMs were photopatterned using a 500 W Hg arc lamp. The patterning process is strongly dependent on the wavelength of light used. When an unfiltered arc lamp is employed, IR light impinges on the sample and causes considerable sample heating. Methyl-terminated SAMs with less than 14 carbons in the chain melt at the temperatures reached and become very disordered and so can be easily displaced by a second SAM. This leads to significant pattern degradation ("erosion"). SAMs with greater than 14 carbons undergo a transition to an incommensurate phase but remain stable on the surface, and the pattern is retained. When the IR light is filtered out, a different behavior is observed. UV-photopatterned methyl-terminated SAMs with 10 carbons in the chain are stable. Terminal group interactions, such as H-bonding, provide extra stabilization energy during photopatterning, so some patterns with shorter carbon chains may also be stable. The displacement of the photooxidized SAMs on the patterned surface follows kinetics similar to that of large-area SAM formation.