Abstract. We studied the influence of 30 keV Ga + -ions -commonly used in focused ion beam (FIB) devices -on the transport properties of thin crystalline graphite flake, La 0.7 Ca 0.3 MnO 3 and Co thin films. The changes of the electrical resistance were measured in-situ during irradiation and also the temperature and magnetic field dependence before and after irradiation. Our results show that the transport properties of these materials strongly change at Ga + fluences much below those used for patterning and ion beam induced deposition (IBID), limiting seriously the use of FIB when the intrinsic properties of the materials of interest are of importance. We present a method that can be used to protect the sample as well as to produce selectively irradiation-induced changes.