We report the structure, optical properties and surface morphology of Si(100) supported molecular multilayers resulting from a layer-by-layer (LbL) fabrication method utilizing copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), also known as "click" chemistry. Molecular based multilayer films comprised of 5,10,15,20-tetra(4-ethynylphenyl)porphyrinzinc(II) (1),and either 1,3,5-tris(azidomethyl)benzene (2) or 4,4'-diazido-2,2'-stilbenedisulfonic acid disodium salt (3) as a linker layer,displayed linear growth properties up to 19 bilayers. With a high,degree of linearity, specular X-ray reflectivity (XRR) measurements yield an average thickness of 1.87 nm/bilayer for multilayers of 1 and 2 and 241 nm/bilayer for multilayers of 1 and 3. Surface roughnesses as determined by XRR data fitting were found to increase with the number of layers and generally were around 12% of the film thickness. Tapping mode AFM measurements confirm the continuous nature of the thin films with roughness values,slightly larger than those determined from XRR Spectroscopic ellipsometry measurements utilizing a Cauchy model mirror the XRR data for multilayer growth but with a slightly higher thickness per bilayer. Modeling of the ellipsometric data over the full visible region using an oscillator model produces an absorption profile closely resembling that of a multilayer grown on silica glass. Comparing intramolecular distances from DFT modeling with experimental film thicknesses, the average molecular growth angles were estimated between 40 degrees and 70 degrees with respect to the substrate surface depending on the bonding configuration.