X-ray photoelectron spectroscopy (XPS) may be suseful to elucidate the kind of bonding between the substrate and film. However the film should be thin ( < 5nm) enough as the depth of analysis using XPS is limited.
Chemical bondings can be studied from Raman or FTIR spect analysis. In some cases raman spec with point or area mapping are also used. XPS with depth profiling is also a good option.
XPS is a very powerful technique for this purpose. You can obtain very detailed information about the chemical bonding in the interface region. However, since XPS only probes the surface you will need to sputter etch your samples to reach the desired depth ("depth profiling"). Sputter etching will affect the chemical bonding in your film and you need to be careful when interpreting the results. Much like you have a collision cascade in your sputter target when you deposit your film, you also have a collision cascade in your precious film when you do sputter etching. The lower sputter energy you use, the better quality of your spectra. The drawback is a much lower sputter rate, leading to a very long total analysis time.
If the polymer film is thin, and the sputtered film is metallic, PM-IRRAS can be a good option. It gives information on what is present at the interface only.
Really, the best techniques are for Photoelectron Spectroscopy X-ray (XPS) for allows the determination of the chemical composition of the surface of his material. You can obtain very detailed information in the interface region about the chemical bonding.
Raman or FTIR Spectroscopy allows to evaluate the quality of the films.
If the film comprises active chemical elements capable of interacting with chemical elements of the polymer, the formation of carbides, etc. is possible. In this case one can use a low-energy part of the Auger spectrum and using AES conduct local structural chemical analysis of the interface.
I am still wondering if you know about studies done already about this matter in very thin films (around 10 nm). The idea is to activate/functionalize a polymer surface in order to determine the bonding between the polymer and a sputtered film. In case of XPS as you said, the analisis has to be done carefully due to the depth of the measurement. Moreover, if the chemical bonds are done by C-O groups with the film, the analisis would be difficult as the oxidation of the film after the sputtering process will affect the measurement. In that case I wont be able to distinguish between the bonding in the interface and the surface of the sputtered film.
I would appreciate if you know about studies already done.