Self-assembled monolayers of amino-undecanethiol and perfluoro-decanethiol are studied by atom probe tomography based on laser-assisted controlled field desorption. In the case of hydrogenated chains the identification of detected molecular species is difficult because of residual hydrocarbons. By contrast, fractions of the fluorinated chains can be unequivocally identified. Although chemically similar, the evaporation of both chains appears in significantly different molecular fractions. For the fluorinated chains, a well-ordered evaporation sequence is determined that allows conclusions to be drawn about the strength of bonds under field conditions and may lay the basis for the future numerical reconstruction of the chemical structure of such films.