Thin films of crude oil samples were prepared for atomic force microscopy (AFM) analysis on the gold substrate. Sample preparation involved evaporation during a long (24 h) but mild thermal exposure (80 °C). Fourier transform infrared (FTIR) microscopy (reflectance spectroscopy) was employed to determinate the quality of the thin film surface, before the morphology characterization. The surface reflectance spectra were compared to direct transmittance FTIR of liquid oil samples. The two FTIR techniques showed different spectral characteristics related to oxygenated functionalities. This clearly indicated that the surface of the thin films of the oil samples prepared for AFM is oxidized. Oil samples of different origin show different degrees of oxidation seen by the development of carboxylic acid vibrations at 1750 cm-1 as well as vibrations in the 1300−1100 cm-1 region. The relative degree of oxidation state was compared to surface morphology data by AFM previously reported. The reported results emphasize the advantage of complementary techniques (AFM/FTIR microscopy) in the analysis of petroleum thin films that should be considered during analysis and interpretation of this type of data.