Self-assembled monolayers (SAMs) are widely used to modify the interfacial properties of solid surfaces in either a homogeneous or a patterned manner. One of the many techniques developed for patterning SAMs involves heating the surface with a focused laser beam. Localized heating can result in pattern formation through either the ablation of both the solid substrate and the SAM (chemically nonspecific patterning) or, at lower temperatures, the selective breaking of the chemical bonds between the SAM and the substrate (chemically specific patterning). The latter method is termed chemically specific laser-induced patterning and is demonstrated for alkanethiol monolayers on gold (Au). In this report, the interplay between alkanethiol desorption and nanoscale Au ablation is studied using atomic force microscopy to image both the topographical and the chemical features of laser patterned areas. Frequently the two processes occur simultaneously but with different spatial extents, as predicted theoretically, due to their different threshold temperatures. By tuning the exposure conditions (laser power and irradiation time), parameters are established where local heating causes alkanethiol desorption without any Au ablation, thus, allowing chemically specific desorption and patterning of alkanethiol SAMs. This allows chemical patterns to be created without changes in the surface topography. Using scanning electron microscopy, a linear dependence of pattern size on irradiation time is demonstrated for circular features 0.5-1 microm in diameter.