Self-assembled monolayers (SAM) are promising building blocks for the optimization of a large variety of systems both on the nano- and on the microscale. Among other applications, SAM are often used as protective coating or friction modifiers. In this work, we have used hexadecanethiol SAM on Au(111) as a model system and studied the different mechanisms of energy dissipation during temperature and velocity dependent friction force microscopy (FFM). In a number of cases, the SAM remained stable during atomic force microscopy experiments and friction-velocity isotherms related dissipation to an activation energy. In other cases, friction experiments lead to an irreversible deterioration of the SAM. This can rather be associated with the general SAM structure that was analyzed by scanning tunneling microscopy and showed a large variety of potential breakdown points like, for example, grain boundaries, step edges, or substrate-related holes in the SAM.