Titania nanotube arrays with their enormous surface area are the subject of much attention in diverse fields of research. In the present work, we show that not only 60 keV and 150 keV ion bombardment of amorphous titania nanotube arrays yields defect creation within the tube walls, but it also changes the surface morphology: the surface relaxes and smoothens in accordance with a curvature-driven surface material’s transport mechanism, which is mediated by radiation-induced viscous flow or radiation-enhanced surface diffusion, while the nanotubes act as additional sinks for the particle surface currents. These effects occur independently of the ion species: both carbon and neon ion bombardments result in comparable surface relaxation responses initiated by an ion energy of 60 keV at a fluence of 1 × 1016 ions/cm2. Using atomic force microscopy and contact angle measurements, we thoroughly study the relaxation effects on the surface topography and surface free energy, respectively. Moreover, surface relaxation is accompanied by further amorphization in surface-near regions and a reduction in the mass density, as demonstrated by Raman spectroscopy and X-ray reflectivity. Since ion bombardment can be performed on global and local scales, it constitutes a versatile tool to achieve well-defined and tunable topographies and distinct surface characteristics. Hence, different types of nanotube arrays can be modified for various applications.