Swift heavy ion beam-based lithography using masks of self-assembled materials has been applied for transferring well-ordered micro- and nanopatterns to rutile TiO2 single crystals. As the induced damage has a high etching selectivity the patterns can be developed in HF with very high contrast. Here we present resulting patterns when using a mask of self-ordered silica spheres. Since the obtained structures are replicas of the mass distribution of the applied mask, the shape and size of resulting structures depend on the geometric configuration of the silica sphere layers. In addition, the resulting pattern can be tuned by varying the applied ion energy and fluence. Direct modifications of the optical properties of TiO2 in a well-defined pattern are also presented.