As Jürgen Weippert said, Spectroscopy Ellipsometry is one of the best techniques to obtain the thickness, roughness, and parameters of thin films.
You can also use AFM to obtain information about thickness (you can deposit your film and use a tape that does not leave residues on the substrate to create a gap between film and substrate, then measure it).
If your film is thick enough, you can perform SEM cross-section analysis.
However, I strongly advise the use of ellipsometry.