The paper describes a set of simple experiments performed to develop an optical model to describe Si/SiO(2) substrates coated with two transparent films of carbon nanotubes. The final goal is to use such optical model to investigate the interaction of proteins with carbon nanotubes. Experiments were performed to assess light reflection as a function of the wavelength or angle of incidence using two substrates (same material, different amounts) composed of oxidized carbon nanotubes. The experimental results indicate that the selected carbon nanotubes layers are anisotropic and significantly different from each other. Experiments performed by spectroscopic ellipsometry (as a function of the wavelength and incident angle) enabled the development of an Effective Medium Approximation model consisting in a two-fraction phase (arc-evaporated carbon and void space). Furthermore, the model enabled calculating the amount of protein adsorbed on the surface of the carbon nanotubes film.