Self-assembled monolayers (SAMs) of n-alkanethiol molecules adsorbed onto Au(111) substrates act as lithographic resists, which can be selectively patterned using scanning tunneling microscopy (STM). We previously provided evidence that patterning is the result of faradaic electrochemical processes. Here, we provide a more detailed model for the patterning mechanism that involves penetration of the tip into the SAM, concerted SAM disruption, and subsequent SAM removal arising from electrochemical processes. Experiments, and a detailed analysis of the patterned features, are consistent with this model. Other key results of this study include the following : (1) the electrochemical nature of the patterning process defines the resolution of STM patterning under the conditions used in this study; (2) lithographically defined patterns are dimensionally stable for several days; (3) the STM tip penetrates the monolayer and very slowly modifies it regardless of bias and tunneling current.