This work reports a procedure to modify the surface nanostructure of TiO2 anatase thin films through ion beam irradiation with energies in the keV range. Irradiation with N+ ions leads to the formation of a layer with voids at a depth similar to the ion-projected range. By setting the ion-projected range a few tens of nanometers below the surface of the film, well-ordered nanorods appear aligned with the angle of incidence of the ion beam. Slightly different results were obtained by using heavier (S+) and lighter (B+) ions under similar conditions.