Low surface energy coatings and films are needed to minimize stiction, high friction, and wear of the oxide-terminated silicon-based microelectromechanical systems (MEMSs) to ensure reliable device function. One common approach is to deposit self-assembled monolayer (SAM) films of molecules possessing a reactive silane head group and low energy pendant chain to cover the complex structures used in MEMS devices. The composition of these films is difficult to characterize and quantify. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is an excellent tool for characterizing these types of films because of its ability to detect small quantities of surface species at high spatial resolution and surface sensitivity; however, interpretation of the spectral data generated is complex and challenging. We are using the combination of x-ray Photoelectron Spectrometry and ToF-SIMS to detect and quantify a fluorocarbon-based SAM on Si coupons and on MEMS devices. Unexpected fragmentation caused by the interaction of the primary ion beam with the fluorocarbon chain in contact with the Si surface creates ions whose presence is not intuitive. We can account for these ion fragments and use them to aid in quantifying the film composition. Our methods include the use of coverage-dependent fragmentation signatures along with the application of multivariate statistical techniques to establish the covariance in these signatures. (c) 2006 American Vacuum Society.