We present grazing-incidence Fourier transform infrared and AFM data of Au, Al, and Ti vapor-deposited onto self-assembled monolayers (SAMs) of conjugated mono- and dithiols. SAMs of 4,4"'-dimercapto-p-quaterphenyl, 4,4"-dimercapto-p-terphenyl, and 4,4'-dimereapto-p-biphenyl have reactive thiols at the SAM/vacuum interface that interact with vapor-deposited An or Al atoms, preventing metal penetration. Conjugated monothiols lack such metal blocking groups, and metals (An, Al) can penetrate into their SAMs. Vapor deposition of Ti onto conjugated mono- and dithiol SAMs and onto hexadecanethiol SAMs destroys the monolayers.