The use of focused ion beams, whilst permitting the targetted preparation of thin specimens for Transmission Electron Microscopy, also results in modification of the material to be investigated as a result of energy being transferred into the material. This undesirable effect is normally limited to the surface of the material, which is particularly unfavourably orientated towards the impinging ion beam. If the crystal structure and composition of areas close to the surface of such specimens need to be characterised, protective layers may be used. However, those layers, depending on the applied deposition technique, may interact with the sample surface as well thus affecting the results of the analysis. In the work presented here, the possible interactions which might occur between the various protective coatings of ion-beam deposited Platinum, electron beam deposited Platinum, Silicon Oxide or adhesively bonded Gold foil and the subsequent FIB-preparation of the oxide layers on Ni-Ti alloys are investigated, with respect to and how these might affect the TEM-images obtained of areas close to the surface of such specimens. It is shown that the use of adhesively bonded Gold foil as a protective coating, in particular, permits comprehensive characterisation of the surface, including the use of high-resolution TEM, to be carried out, up to the surface of the Oxide layer itself.