New nanocomposite thin films were prepared by spin coating technique from polystyrene (PS) and montmorillonite (MMT) modified with perfluoropolyether cationic ammonium salts (FOMMT). The coating thickness was tuned by changing the solution concentration, and it was measured by the scratching method with atomic force microscopy (AFM). Demodulation AFM images of the higher thickness (> 100 nm) PS/FOMMT nanocomposite coating do not show any phase difference suggesting the formation of a homogeneous structure, while the corresponding demodulation image of the lower thickness (ca. 60 nm) PS/FOMMT nanocomposite film revealed the presence of two different phases, which may be attributed to fluoromodified clays and polystyrene. Surface characterization was made through contact angle (CA) measurements and it showed unexpectedly low surface tension dispersive component gamma (s) (d) (around 12 mN/m) and a very high polar components gamma (s) (d) (50 mN/m) in the case of the lower thickness PS/FOMMT nanocomposite coating.