We have used swift heavy-ion beam based lithography to create patterned bio-functional surfaces on rutile TiO2 single crystals. The applied lithography method generates a permanent and well defined periodic structure of micrometre sized square holes having nanostructured TiO2 surfaces, presenting different physical and chemical properties compared to the surrounding rutile single crystal surface. On the patterned substrates selective binding of oligonucleotides molecules is possible at the surfaces of the holes. This immobilisation process is only being controlled by UV light exposure. The patterned transparent substrates are compatible with fluorescence detection techniques, are mechanically robust, have a high tolerance to extreme chemical and temperature environments, and apparently do not degrade after ten cycles of use. These qualities make the patterned TiO2 substrates useful for potential biosensor applications. ; Funding Agencies|Carl Tryggers Foundation; VR Linneaus grant LiLi-NFM; EU Project WATER [316082]; Madri+d Foundation; Genoma Espana Foundation; European community; European Research infrastructure EUMINAfab [FP7-226460]; FP7 specific programme Capacities [FP7-226460]; Karlsruhe Nano Micro Facility (KNMF); Helmholtz Research Infrastructure at Karlsruhe Institute of Technology (KIT); Centre for Research on Adaptative Nanostructures and Nanodevices (CRANN) a Science Foundation Ireland based in Trinity College Dublin