Modeling and experimental reflectance spectra of porous silicon single layers at different steps of functionalization and protein grafting process are adjusted in order to determine the volume fraction of the biomolecules attached to the internal pore surface. This method is applied in order to control the efficiency of the chemical functionalization process of porous silicon single layers. Using results from single porous silicon layer study, theoretical microcavity is simulated at each step of the functionalization process. The calculated reflectance spectrum is in good agreement to the experimental one. Therefore the single layers study can be applied to multilayer structures and can be adapted for other optical structures such as waveguides, interferometers for biosensing applications.