The effect of atmospheric pressure He plasma on the molecular structure of polyethylene terephthalate (PET) has been investigated. The plasma composition was analyzed using optical emission spectroscopy. In addition to strong He emission lines, lines due to O and N radicals were also detected. The change in the molecular structure of the PET film surface was investigated using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. It was found that plasma irradiation led to oxidation and degradation of the surface due to chemical and physical effects of the active species. The results demonstrate the feasibility of observing the interaction of plasma with organic material on a local scale.