Depth resolved investigations of defects and their evolution upon inter-diffusion have been carried out on Al/Ge thin film bilayers, using concurrent measurements of positron beam based Doppler broadening lineshape and secondary ion mass spectrometry (SIMS) profiles. Measurements have been made on the as-grown film and films annealed at various temperatures from 370 to 670 K. SIMS studies establish the occurrence of extensive intermixing of the Al and Ge layers beyond 370 K. It is found that there is an asymmetric diffusion across the interface, with Ge being the dominant diffusing species. The intermixed Al/Ge region formed in the near-surface layers of the sample annealed at 670 K shows Ge precipitation, as confirmed by electron microscopy and SIMS imaging. Analysis of the Doppler broadening line shape variation, together with the SIMS concentration profiles, indicates increased production of small vacancy clusters at the Al/Ge interface around 520 K, brought about by the enhanced diffusion of Ge. The interfacial vacancy structure is inferred to be a tri-vacancy cluster.