Polarized attenuated total reflection (AIR) Fourier transform infrared (FTIR) spectroscopy was utilized to characterize the three-dimensional orientation of polymer chains near highly anisotropic surfaces generated by uniaxial drawing. A versatile method was proposed to analyze the molecular orientation of the polymers by combining the experimental refractive indices and optimized contact pressure by an anvil for solving the optical contact problem. This method is effective even when changes in the molecular orientation along the thickness direction caused by drawing are remarkable. In addition, this method enables quantitative comparison of the molecular orientation among different polymers in the same coordinate system. From the molecular orientation analysis of poly (ethylene terephthalate) (PET) and poly (ethylene naphthalate) (PEN), it was revealed that this method has a broader range of applications with high accuracy in estimating the molecular orientation of polymers compared with the conventional methods. The significant changes in the molecular orientation caused by uniaxial and biaxial drawing of PET and PEN films were quantitatively analyzed, and the reasons for the significant in-plane orientation of PEN chains on the film plane are discussed. In addition, the difference in the molecular orientation between both sides of the films was also demonstrated. (C) 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 870-879, 2010