The Centre d'Etudes Nucléaires de Bordeaux-Gradignan (CENBG) will soon be equipped with a new state of the art accelerator facility including a single-ended HVEE® 3.5 MV Singletron. Its performance in terms of brightness and energy stability will provide the unique opportunity to develop a high spatial resolution nanobeam line. The actual microbeam line dedicated to ion beam analysis (scanning transmission ion microscopy, particle induced X-ray emission and Rutherford backscattering spectrometry) and to cellular irradiation will be reinstalled on the new machine. In this paper, expected performances of the two beam lines are presented from ray tracing simulations using the Geant4 toolkit, capabilities of which at the sub-micron scale have been investigated and validated previously.