Generally speaking, you can replace extremely thin films in HFSS with either an impedance boundary condition or a layered impedance boundary. Consult the online help for more information. The issue with thin objects is not that HFSS won't do a good job of meshing the films. It is the fact then when you get long,skinny tetrahedra, the results become less accurate. This has to do with the fundamental method underlying HFSS.
One way around this is to select the thin layer, and go to HFSS / Mesh Operations / Assign / Surface Approximation. From there, set the Aspect Ratio setting for about a 5:1 ratio. This will drive up the number of tets, so you also might want to invoke the Iterative solver in the Adaptive Setup options to reduce the memory required. One other option would be to change the order of the elements to Mixed to make the meshing more efficient.