Self-assembled monolayers (SAMs) formed from alkyl-terminated, CF3-terminated, CF3CF2-terminated, and C10F21-terminated alkanethiolates on gold substrates were examined by low-energy (eV) ion-surface collisions to determine the impact of varying the degree of fluorination of the thiolate tail group. The fluorine-terminated SAMs are compared and contrasted to previously examined CF3-terminated Langmuir-Blodgett films. Polyatomic (M+. for benzene and pyrazine) and atomic (Mo+. and Cr+.) ions were collided with the different SAM films at various collision energies (20-70 eV). Data indicate that substitution of CH3 with CF3 as the terminal group has a substantial influence on the ion-surface interactions, including energy transfer (fragmentation), electron transfer (neutralization), and atom/group transfer (reaction). However, slight penetration into a depth of the film is apparent and illustrated with the formation of certain ion-surface reaction products and the intensities of those products. This penetration has a noticeable effect on low-energy ion-surface collisions. Also, results for a series of CF3(CH2)(n)S-Au films (where n = 12, 13, 14, 15) illustrate that ion-surface reactions vary with the orientation of the fluorine atoms that are present in the terminal group. The results from collisions of low-energy ions with these relatively well-defined surfaces allow further characterization of the collision events that have the potential to become valuable tools in surface analysis.