Surface elemental and structural characterization of hexadecanethiol and heptadecanethiol (C and C for short) and 16,16,16-trifluorohexadecanethiol (FC) self-assembled monolayers (SAMs) on a Au111 surface have been obtained from time-of-flight scattering and recoiling spectrometry. The clean Au surface was also characterized in order to identify the azimuthal orientation of the SAMs with respect to the substrate. Classical ion trajectory simulations were used to relate the experimental scattering and recoiling data to the surface structure. The scattered and recoiled atoms originate from the outermost five-six atomic layers, and azimuthal anisotropy was observed in the measurements. The results provide a model for the SAMs in which the alkyl chains chemisorb with the S atoms situated above the face-centered-cubic (fcc) threefold sites of the Au111 surface to form a continuous film with a (√3×√3)R30° structure that fully covers the Au surface. The orientation of the molecular axis azimuth of the SAMs relative to the Au azimuthal directions was determined. The data indicate that the molecular chains have specific tilt and twist angles relative to the Au surface and six coexisting domains resulting from the six equivalent tilt directions of the molecular axis. Dramatic changes in the anisotropic patterns of the ion scattering azimuthal scans from the surfaces of the SAMs with different terminations were observed. These phenomena result from the different tilt angles of the CH and CF groups. The data are consistent with free rotation of both the CH and CF groups. The C SAM exhibited the best azimuthal features and was more resistant to radiation damage from the incident Ar scattering beam than the other films. Due to the tilt angle of the SAMs, an "ion's eye view" of the structure, i.e., the positions of the atomic cores as experienced by the incoming keV ions, reveals a regular array of sloping cavities within each unit cell.