This work focuses on the quantitative application of spectroscopic ellipsometry to the study of optical properties and thickness of self assembled monolayers (SAMs) of phenyl selenide deposited from the liquid phase on gold. STM, XPS and cyclic voltammetry measurements provide additional chemical and morphological characterization of the SAMs. While routine ellipsometry analysis of SAMs often relies on the film-induced δΔ change in the Δ ellipsometric angle and discards SAM-substrate interface effects, the present data show a distinctive behaviour of the δΨ data that we assign to interface effects, stronger than those previously found for densely packed alkanethiol SAMs. An inaccurate modelling of the variations in Ψ related to the nano-structured SAM-substrate interface leads to a large overestimation of the film thickness. A simple model, which takes into account an effective approximation for the interface layer between the film and the substrate, and the molecular optical absorptions, provides a good agreement between the data and a reliable thickness estimate of the SAM.