This question is probably known, as I am an undergraduate reaching into a non-familiar field. My current studies require me to know the bonding characteristics between two or three thin layers of metals (and alloys); Copper, Chromium, NiCr, Indium-Bismuth for example.
There is a clutter of various spectroscopy acronyms, EDS, EELS, XPS, XRD, PES, TEM to name a few, and the literature is as broad as their respective names. Is there an easy answer, and one simple technique? Or must two techniques be carried out in duet?
For thin film analysis and for any surface analysis there isn't a smoking gun instrument that allows for complete analysis (organic chemists have the wonderful NMR instrument that allows for nearly complete characterization of their respective compound). Since your materials are on the nanometer range I would suggest Spectroscopic Ellipsometry (this will allow for thickness measurements, refractive index, and extinction coefficients), XRD will allow for crystal grain orientation, EELS will give you an idea of bonding between the layers albeit that requires fitting to models.
If you have access to a useful database, XPS could be helpful too. Nevertheless, your key point is the sample thickness. If your investigated layers are very thin some of the mentioned techniques won't be successful. EDX for instance is not surface sensitive and looks "through" the first nm. XRD requires a reasonable amount of crystal (and crystallinity) to separate real signals from background noise.
In general, I don't think there is a general positive answer to your question. Discuss with people handling the machines by explaining them in detail what you expect. The more you know about your samples, the better results you'll get. Furthermore, those people will be able to explain you more precise what the resolution limits of their machine is.
The formation of intermetallic bonds can be nicely followed by EXAFS and XANES (X_ray absorption spectroscopy). The short range order structure that is probed by those techniques is completely different for the different phases, and therefore it can be used as a fingerprint. See e.g. the work by Iztok Arcon and coworkers (J. Synchrotron Rad. 8 (2001) 493 or similar) Check the literature! Good luck, Dirk
For thin films you could also try Auger electron spectroscopy. Some metallic compounds show complete different spectra than the linear combination of the spectra of the pure metals. I measured this effect for example on MgZn2 and Fe2Al5. Unfortunately it it not always working, for example the ZnFe compounds have the same spectra as the elements.
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