A detailed study of the self-assembly and coverage by 1-nonanethiol of sputtered Au surfaces using molecular resolution atomic force microscopy (AFM) and scanning tunneling microscopy (STM) is presented. The monolayer self-assembles on a smooth Au surface composed predominantly of {111} oriented grains. The domains of the alkanethiol monolayer are observed with sizes typically of 5-25 nm, and multiple molecular domains can exist within one An grain. STM imaging shows that the (4 x 2) superlattice structure is observed as a (3 x 2root3) structure when imaged under noncontact AFM conditions. The 1-nonanethiol molecules reside in the threefold hollow sites of the Au{111} lattice and aligned along its [112] lattice vectors. The self-assembled monolayer (SAM) contains many nonuniformities such as pinholes, domain boundaries, and monatomic depressions which are present in the An surface prior to SAM adsorption. The detailed observations demonstrate limitations to the application of 1-nonanethiol as a resist in atomic nanolithography experiments to feature sizes of similar to20 nm.