Topological insulator (Bi0.06Sb0.94)(2)Te-3 thin films grown by molecular beam epitaxy have been capped in-situ with a 2 nm Al film to conserve the pristine topological surface states. Subsequently, a shadow mask-structured by means of focus ion beam - was in-situ placed underneath the sample to deposit a thick layer of Al on well-defined microscopically small areas. The 2 nm thin Al layer fully oxidizes after exposure to air and in this way protects the TI surface from degradation. The thick Al layer remains metallic underneath a 3-4 nm thick native oxide layer and therefore serves as (super-) conducting contacts. Superconductor-Topological Insulator-Superconductor junctions with lateral dimensions in the nm range have then been fabricated via an alternative stencil lithography technique. Despite the in-situ deposition, transport measurements and transmission electron microscope analysis indicate a low transparency, due to an intermixed region at the interface between topological insulator thin film and metallic Al. (C) 2017 Elsevier B.V. All rights reserved.