A molecular beam epitaxy (MBE) system used for epitaxial growth of rare earth (Eu, Sm and Nd) compounds on CdTe is described. Owing to the high reactivity of the films, it appeared fruitful to connect this apparatus to a 2.5 MeV van de Graaff accelerator, allowing an in situ structural characterization of the samples by Rutherford backscattering spectrometry and ion channelling analysis. Effusion cell flux calibration, homogeneity and thickness layer measurements are presented. For the first steps of the rare earth deposition, the correlation of thickness measurements to reflection high energy electron diffraction patterns is shown. Interfacial defect studies by ion channelling during CdTe growth on Cd1-xZnxTe are also reported.