We demonstrate that ATR-FTIR spectroscopy can be used to record high-quality vibrational spectra of molecules at buried interfaces in metal-molecule-silicon and metal-molecule-metal junctions. This provides quantitative information on the structure and conformation of molecules at buried interfaces, an issue of critical importance to molecular electronics. In the model systems of Au on octadecyltrichlorosilane self-assembled monolayer on Si or mecaptohexadecanoic acid multilayers on Au-covered Si, ATR-FTIR suggests that metal deposition leads to not only conformational disorder within the film but also the direct interaction of metal atoms/clusters with alkyl backbones.