The structure of self-assembled monolayers (SAMs) of various fluorinated disulfides, perfluoroalkylamide thiols, and a mixed alkyl perfluoroalkylamide disulfide on sputtered gold was studied by atomic force microscopy (AFM). AFM, performed both in air and in ethanol, revealed the monolayer structure with molecular resolution on the polycrystalline gold substrates. For all partially fluorinated disulfides containing ester groups, a hexagonal lattice with a lattice constant of 5.8-5.9 Å was found. A mixed alkyl perfluoroalkylamide disulfide formed a hexagonal lattice of a slightly larger lattice constant (6.1 Å), whereas the lattice observed for fluorinated thiols containing an amide group was either hexagonal (5.7-5.8 Å) or distorted hexatic (5.6, 6.2, 5.6 Å), depending on the length of the perfluoroalkane segment and the imaging force. The observed deviation from hexagonal symmetry is attributed to the distorting effect of hydrogen bonding between neighboring amide groups within the monolayer. For short perfluoroalkane segments the distortion is observed at low imaging forces, whereas for long perfluoroalkane segments significantly higher imaging forces are necessary in order to observe the distortion. The force dependence of the measured lattice symmetries for different chain lengths suggests that the AFM tip penetrates into the SAM and probes at least partially the interior of the SAM.