Applications of ion beam techniques (IBA and IBMM) on nanoscaled thin films of selected materials (e.g. magnetite Fe₃O₄, uranium nitride UN) are presented. 1 MeV Ar⁺ and Kr⁺ ion beam with different ion fluences in the range of 10¹⁵–10¹⁷ ions cm⁻² have been used to modify the film interfaces. Selected heterostructure interfaces were treated by subsequent thermal annealing. By analyzing the results obtained for the films in three different states (as-deposition, after annealing and after ion irradiation), the effects of ion beam mixing and interdiffusion were determined.