The physical properties of thin multilayer structures are deeply related to the crystalline quality and stoichiometry of the films. The interface roughness/mixing require a detailed study to determine its influence on the growth processes and surface topography. This is an important aspect when we have lattice mismatch between the superconducting thin-films and the substrates, and a high reliability/reproducibility is required as for large array microcalorimeter applications, as in the case of the MARE experiment, designed to measure the mass of the neutrino with sub-eV sensitivity by measuring the beta decay of 187Re with cryogenic microcalorimeters. Ion beam analysis techniques are ideal to determine the thickness and concentration profiles of the chemical species in ultra-thin films. Here we present the results on the Ir-based superconducting films deposited on Si-substrates based on systematic investigations of the concentration depth profiles of the multilayer structure using 2.0 MeV 4He+ ions for high resolution Rutherford Backscattering Spectrometry combined with X-Ray Reflectrometry to evaluate the interface/roughness mixing and the crystalline quality in the TES prototypes.