Fatty acids and their derivatives have been used as model organic friction modifiers for almost a century, but there is still debate as to the nature of the boundary films that they form on rubbed surfaces. In this study, in situ liquid cell atomic force microscopy (AFM) is used to monitor the self-assembly of boundary films from solutions of fatty acids in alkanes on to mica surfaces. Because the mica surfaces are wholly immersed in solution, it is possible to study directly changes in the morphology and friction of these films over time and during heating and cooling. It has been found that stearic acid and elaidic acid, which are able to adopt linear molecular configurations, form irregular islands on mica that are tens to hundreds of microns in diameter and typically 1.6 nm thick, corresponding to domains of tilted single monolayers. At a relatively high concentration of 0.01 M, stearic acid in hexadecane forms an almost complete monolayer, but at lower concentrations, in dodecane solution and for elaidic acid solutions, these films remain incomplete after prolonged immersion of more than a day. The films formed by fatty acids on mica are displaced by repeated scanning in contact mode AFM but can be imaged without damage using tapping mode AFM. Rubbed quartz surfaces from a sliding ball-on-disc test were also scanned ex situ using AFM, and these showed that stearic acid forms similar monolayer island films on quartz in macro-scale friction experiments as are found on mica. Oleic acid solutions behave quite differently from stearic acid and elaidic acid, forming irregular globular films on both mica and rubbed quartz surfaces. This is believed to be because its cis-double bond geometry means that, unlike its trans-isomer elaidic acid or saturated stearic acid, it is unable to adopt a linear molecular configuration and so is less able to form close-packed monolayers.