Two methods—attenuated total reflection Fourier infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS)—have been used to analyze the chemical structure of polytetrafluorethylene (PTFE) thin coatings deposited by pulsed laser (PLD) and pulsed electron beam (PED) ablations. The volume of the analyzed materials is significantly different in these techniques which can be of great importance in the characterization of highly heterogeneous thin films. Optical microscopy, atomic force microscopy (AFM) and scanning electron microscopy (SEM) have been additionally used to examine the coating surface morphology. The studies have shown that in the case of thin polymer coatings deposited by physical methods, the application for chemical structure evaluation of complementary techniques, with different surface sensitivity, together with the use of surface topography imaging, provide unique insight into the film morphology. The results can provide information contributing to an in-depth understanding of the deposition mechanism of polymer coatings.