We report studies on the modifications induced by the evaporation of copper overlayers on a self-assembled monolayer (SAM) of the oligo(phenylene-ethynyl) dithiol, 1-thio-4-[4'-[(4'-thio)phenylethynyl]-1'-ethynyl] -benzene (TTPEB). These SAMs were characterized after deposition from a tetrahydrofuran solution on polycrystalline gold substrates and after copper evaporation and its subsequent removal by nitric acid. Monolayers were studied via cyclic voltammetry (CV), UV-vis multiwavelength ellipsometry, external reflectance infrared (IR) spectroscopy, and ion scattering spectroscopy (ISS). The results obtained indicate that TTPEB SAMs display the same packing characteristics before and after copper evaporation and removal. However, as shown by IR spectroscopy, the monolayers undergo a reorganization process that involves an increase in tilt angle accompanied by rotation of aromatic rings that results in a decrease in the average molecular twist angle. ISS data suggest that copper diffuses through the monolayer after copper evaporation, a result that is significant for applications of this molecule in molecular electronic devices.