Self-assembled monolayers (SAMs) are commonly produced by immersing substrates in organic solutions containing trichlorosilane coupling agents. Unfortunately, such deposition solutions can also form alternate structures, including inverse micelles and lamellar phases. The formation of alternate phases is one reason for the sensitivity of SAM depositions to factors such as the water content of the deposition solvent. if such phases are present, the performance of thin films used for applications such as the minimization of friction and stiction in micromachines can be seriously compromised. Inverse micelle formation has been studied in detail for depositions involving 1H,1H,2H,2H-perfluorodecyltrichlorosilane (FDTS) in isooctane, Nuclear magnetic resonance experiments have been used to monitor the kinetics of hydrolysis and condensation reactions between water and FDTS. Light-scattering experiments show that there is a burst of nucleation at a critical concentration of hydrolyzed FDTS to form high concentrations of spherical agglomerates. Atomic force microscopy results show that the agglomerates then deposit on substrate surfaces. Deposition conditions leading to monolayer formation involve using deposition times that are short relative to the induction time for agglomeration. After deposition, inverse micelles can be converted into lamellar or monolayer structures with appropriate heat treatments if surface concentrations are relatively low.