We present a comprehensive and structurally correct optical model for layers of nanometer sized gold particles, cross-linked with α,ω-alkane dithiol molecules, HS−(CH2)n−SH with n = 2, 8, 15. The solution requires a two-stage, three-phase effective medium model based on the observed nanostructure of the three constituents, gold, thiol, and voids. Voids and their topology, which were neglected in previous models, prove to be crucial in the explanation of the optical properties.