It is very much dependent on your application and the desired results you are looking for. If you are looking for surface absorption, reflection or general surface and material properties , I suggest COMSOL and CST as they have better multiphysics suites. HFSS is good for designing antennas and radiating structures.
General, you can make cylinderical nano scale structures with material parameters in both of these softwares (CST and HFSS) but then comes the thing that what exactly you want to do and measure from simulations ?