A model organic material, namely the 36-n-alkane hexatriacontane, was etched in a dissymmetrical parallel plate RF plasma reactor and a dual distributed electron cyclotron resonance (DECR) plasma reactor, in different O2-Ar mixtures. A specific attention was paid to the role of the ion bombardment, especially when its effect is combined with the chemically active species created in an oxygen discharge. The discharge was monitored by optical emission spectroscopy (OES). The modifications induced by plasma treatment on the structure of the material were analysed by Fourier transform infrared spectroscopy (FTIR), steric exclusion chromatography (SEC) and composition analysis. We found that the ion bombardment has not only a sputtering effect but also enhances the reaction rate of the chemical species on the layer surface. It appears that plasma treatment leads to cross-linking and recombination with molecules from the room atmosphere.