XRD can usually determine if there is some sort of phase shift in a material. Different orientations of the molecules in a material will have different 2-theta values, even if they are small.
Refractive index might be an issue of hickness dependent density.
For VERY thin films it could be interesting to use synchrotron radiation and do NEXAFS experiments. it is a cute method to determine the orientation of pi* and sigma* states. The more inequivalent sites of the same element you have, the more difficult it may get to interpret the results, though.
There is an excellent book by J. Stöhr covering the topic. the title is "NEXAFS", I think and it appeared with Springer Verlag in the 1990's.
Depending on your choice of substrate, it might be interesting and possible to do such experiments in an x-ray microscope. Check publications of e.g. H. Ade in this respect.
I found that the refractive index measured for ultrathin film (~ 10 nm) using ellipsometry decreases with increasing the incident angle however the thickness of the film unchanged. On the other hand, the refractive index is unchanged with increasing the incident angle for the thick film (~ 100 nm). All films prepared onto Si substrate.
Attenuated Total Reflectance (ATR) infrared spectroscopy is an excellent way of measuring the orientation of a polymer film either towards the air or substrate interface. If you have an easy way of detaching the film from the substrate, then the procedure is simple. Alternatively, one can adjust the details of the ATR beam to vary the degree of penetration of the film over a considerable range. This would one to see variations in concentration of different functionalities as a function of depth, which in turn will suggest whether there is an enrichment of given functionality (e.g. carbonyl, carboxyl, or hydroxyl) near either interface. Schreiber of Ecole Poly in Canada did a lot of work with acrylic polymers and the influence of water on orientation of functionalities about 20 years ago. He found enrichment of polar groups near polar substrates, and reorientations in the presence of water. Look in the literature between 20 and 30 years ago for such studies by other authors. The key words would include ATR, surface (interface) orientation, and surface (interface) enrichment.
Sum Frequency generation spectroscopy has been used to study structure and orientation of water and ionomers or polyelectrolytes in thin films at interfaces. You might find the following papers interesting:
1. "Humidity-Dependent Structure of Surface Water on Perfluorosulfonated Ionomer Thin Film Studied by Sum Frequency Generation Spectroscopy" (Link: http://pubs.acs.org/doi/abs/10.1021/jp907194k)
2. "Interfacial Molecular Structures of Polyelectrolyte Brush in Contact with Dry Nitrogen, Water Vapor, Liquid Water, and Aqueous Electrolyte Solution Studied by Sum Frequency Generation Spectroscopy" (Link: http://pubs.acs.org/doi/abs/10.1021/ja107265q)