Semi-crystalline poly(ethylene terephthalate) (PET) film surfaces were modified with argon and oxygen plasmas by radio-frequency (RF) glow discharge at 240 mTorr/40W; the changes in topography and surface structure were investigated by atomic force microscopy (AFM) in conjunction with specular reflectance of infrared microspectroscopy (IMS). Under our operating conditions, analysis of the AFM images revealed that longer plasma treatment results in significant ablation on the film surface with increasing roughness, regardless of the kind of plasma used. The basic topographies, however, were different depending upon the kind of gas used. The specular reflectance analysis showed that the ablative mechanisms of the argon and oxygen plasma treatments are entirely different with one another. For the Ar-plasma-treated PET surface, no observable difference in the chemical structure was observed before and after plasma treatment. On the other hand, the oxygen-plasma-treated PET surface displays a significant decrease in the number of aliphatic C-H groups. We conclude that a constant removal of material from the PET surface occurs when using the Ar-plasma, whereas preferential etching of aliphatic C-H groups, with respect to, e.g., carbonyl and ether groups, occurs upon oxygen plasma.