We present a comparative study of the structural parameters characterizing thin macromolecular adsorbed films that are obtained from two optical techniques: optical waveguide lightmode spectroscopy (OWLS) and scanning angle reflectometry (SAR). We use polyelectrolyte multilayers and polyelectrolyte multilayers/protein films to perform this study. The comparison between the information obtained with the two methods is possible because the buildup of the polyelectrolyte multilayers is known to become substrate independent after the deposition of the first few polyelectrolyte layers. The analysis of the optical data requires usually to postulate a refractive index profile for the interface. Two profiles have been used: the homogeneous and isotropic monolayer and the bilayer profiles. When the refractive index profile of an adsorbed film is well approximated by a homogeneous and isotropic monolayer, as shown by using an analysis of the deposited films in terms of optical invariants, the two optical techniques lead to similar values for the film thickness and the optical mass. The situation is more complex in the case of the multilayers/protein films for which the calculated parameters can strongly depend upon the refractive index profile that is postulated to analyze the optical data. Whereas the optical mass and, to a lesser extent, the thickness seem fairly model independent for OWLS, they appear to be extremely sensitive to the model for SAR. For proteins deposited on top of the polyelectrolyte film, optical mass and protein thickness were found to be comparable when determined by OWLS and by SAR using the bilayer model. The data analysis of the SAR curves with the monolayer model leads to much larger and even physically unreasonable film thicknesses and optical masses. This was particularly noticeable for proteins having a large size (human serum albumin and fibrinogen), whereas both models lead to similar results for small sized proteins. By means of the different refractive index profiles, we show that great care must be taken in the physicochemical interpretation of the structural parameters determined by these optical techniques.