EPJ Applied Physics 56. 2 (2011): 24021 with kind permission of The European Physical Journal (EPJ) ; A full characterization of plasma polymerized biofunctional films requires the use of multi-analytical approaches to determine the chemical composition, topography and potential interaction mechanisms of such films with biomolecules and cells. In this work we aim at underlining the versatility of ion-based techniques to contribute to the chemical characterization of plasma polymerized surfaces. The simultaneous use of energy recoil detection (ERD) and Rutherford backscattering (RBS) spectroscopies with incident He ions is an example of this versatility. Performing sequential measurements and the use of correlating computing tools for ERD-RBS interpretation allows providing in-depth concentration profiles of light elements, including namely hydrogen. More accurate analysis of light elements in polymer films can be increased by looking for particular ions with resonant backscattering responses (i.e., non-Rutherford Scattering). In particular, proton beams of 1.765 MeV are used to increase the detection of C and N, and particular incidence and detector angles to diminish the Si substrate contribution. These analytical tools have been applied to allylamine films and multi-layers crosslinked in a capacitive plasma onto both Si and porous Si substrates