Atomic force microscopy measurements have been performed in order to study mercury cadmium telluride thin films grown on hybrid substrates by means of a new method based on an isothermal vapor phase epitaxy process (iso-VPE). The morphology of the samples, grown both on sapphire and on silicon 2 in. substrates, was observed at the different steps of the iso-VPE process. In the case of the silicon substrate the absence of interdiffusion with the deposited film was detected by means of a cross sectional atomic force microscopy analysis of the sample. Moreover, the surface quality of the iso-VPE grown thin films has been found to be comparable with that of samples grown on hybrid substrates by means of conventional techniques like liquid phase epitaxy. Fourier-transform infrared measurements were also performed in order to prove the high optical goodness of the samples.