A comparative study of polytetrafluoroethylene (PTFE) surfaces treated by the post-discharge of He and He-O2 plasmas at atmospheric pressure is presented. The characterization of treated PTFE surfaces and the species involved in the surface modification are related. In pure He plasmas, no significant change of the surface has been observed by X-ray photoelectron spectroscopy (XPS), dynamic water contact angles (dWCA) and atomic force microscopy (AFM), in spite of important mass losses recorded. According to these observations, a layer-by-layer physical etching without any preferential orientation is proposed, where the highly energetic helium metastables are the main species responsible for the scission of −(CF2)n− chains. In He−O 2 plasmas, as the density of helium metastables decreases as a function of the oxygen flow rate, the treatment leads to fewer species ejected from the PTFE surfaces (in agreement with mass loss measurements and the detection of fluorinated species onto aluminum foil). However, the dWCA and AFM measurements show an increase in the hydrophobicity and the roughness of the surface. The observed alveolar structures are assumed to be caused by an anisotropic etching where the oxygen atoms etch mainly the amorphous phase.