Self assembly processes have made it possible to prepare organic monolayers with well-defined surface structures and chemistries. The ability to systematically vary the surface structure and chemistry of these self-assembled monolayers (SAMs) provide an excellent method for examining the relationship between the surface properties of a film and its performance in a given application (e.g., cell culture). To develop these relationships requires detailed characterization of the surface composition, molecular structure, orientation, and topography of the films with techniques such as XPS, ToF SIMS, NEXAFS, and STM. How the methods and molecules used to form fluorinated films affect the resulting film structure will be discussed. The degree of ordering and relative orientation in SAMs prepared with perfluoroalkyl thiols depend on the length of the fluorinated tail. Although SAMs prepared from thiols with long perfluoroalkyl tails are highly ordered, their stability is limited by the single point attachment of the Au-S bond. This stability can be increased by using grafted copolymers containing both perfluorinated and alkanethiol side chains to generate multipoint attachment of each polymer chain. However, this method of increasing film stability also results in a decreased degree of film orientation. Typically films prepared using polymers with perfluorinated side chains are highly disordered. Only at high concentrations of perfluoroalkyl side chains (>50%) is any ordering detected in polymeric monolayers. Other methods, such as trifluoroacetic anhydride derivatization of hydroxyl-terminated alkanethiols can also be used to produce fluorinated surfaces. Depending on the derivatization system, the high degree of ordering in the starting SAM can be retained after derivatization.