A variety of techniques were applied to probe for surface modifications and structural changes in thin high TcYBa2Cu3O7-delta (YBCO) superconducting films prepared onto MgO substrates after time of flight heavy ion elastic recoil detection analysis (HERDA). Films have been prepared by ex-situ processing of a spin-coated organic sol-gel precursor. Evidence is provided for the smoothening of the surface of the films accompanied with an amorphisation of the YBCO films in the HERDA spot region. The virgin surface roughness of 30-50 nm could be reduced to 1-2 nm after bombarding the film for a short time with pA current. However, large scale surface roughness on the 200 nm scale remained unchanged. Importantly, the integrity of the superconductor films did not change significantly during HERDA allowing simultaneous measurements of high resolution Y, Cu, Mg and C depth profiles. Further research will utilise the HERDA depth profiling capability for carbon and copper since the copper stoichiometry and fraction of carbon as an impurity are crucial for an understanding of the performance of the YBCO films. (C) 2003 Elsevier B.V. All rights reserved.