The surface treatment of different polymers and their corresponding model surfaces in the flowing afterglow of an oxygen microwave plasma is investigated The concentration profiles of the long-lived species issued from the plasma are measured and calculated in the downstream area. The influence of atomic and singlet molecular, oxygen in tire behavior of different polymers is investigated. It appears that the evolution of the surface energy can be explained by an initiation of the functionalization by the oxygen atoms impinging upon the surface followed by reaction of the radicals formed with molecular oxygen. The concentration of functions at the surface is limited due to their destruction by reaction with oxygen atoms. Furthermore, the functionalization level is higher in the flowing afterglow than in the plasma, without any significant degradation of the polymer surface. Therefore, the treatment in the flowing afterglow is more efficient to increase surface energy, in particular, for polymers which undergo high backbone chain scission.