A thin film (<10 nm) of fine metal clusters (silver or gold) with an island form was deposited on a CaF2 salt plate by slow vacuum thermal evaporation. Molecular layers of stearic acid, p-nitrobenzoic acid, and m-nitrobenzoic acid (p- and m-NBA) were prepared on the thin metal film. The system was then examined by infrared spectroscopy attenuated total reflection (IR-ATR). It was found that through the interaction between the metal islands film and the electric field of the incident IR beam the infrared absorption of the molecule layers adsorbed on the islands was enhanced by a factor of 17. The surface-enhanced IR absorption (SEIRA) also presents a selection rule. This method was then used to study the surface modification with O-2 and NH3 plasma and the plasma polymerization of allylamine. This is the first time that SEIRA has been used in plasma investigations. A model is provided to explain the interactions between the metal islands film and the electric field of the incident IR beam in the SEIRA. The in-plasma-built functional groups can be further used to graft biofunctional molecules for the biomedical industry.