During the last few years, refractive index profiles are being studied more intensively. Several papers have been written about the use of optical methods, spectrophotometry, ellipsometry, together with reverse engineering, these have yielded interesting results. Here we study the differences of a ZrO2 film grown on an amorphous substrate and that of a pre-evaporated layer of another material, Y2O3. In the first run, two glass substrates have been coated with an Y2O3 layer. In the second run a bare glass substrate and the pre-coated Y2O3 have been coated with a ZrO2 layer. Each of the materials used had exactly the same growth conditions for all layers. The only difference was the nature of the substrates. The spectra of R and T of both samples have been used for the optical characterisation. Multisample analysis with gradual introduction of new parameters has been carried out. It was found that for the appropriate modelling of the layer, grown on the pre-coated substrate, introduction of an interface layer between the two materials was necessary. The refractive index profiles of both ZrO2 layers have been determined and discussed.