The electronic transport and gating characteristics in GaAs and Ge nanowires (NWs) are altered significantly following either indirect or direct exposure to a focused Ga+ ion beam (FIB), such as that used to produce Pt electrical contacts to NWs. While these results challenge the assumptions made in some previously reported work relating to the electronic properties of semiconductor NWs using FIB-assisted production of contacts and/or their leads, local electron beam induced deposition is shown to be a reliable and facile route for producing robust electrical contacts to individual vapor phase-grown NWs in a manner that enables study of their actual carrier transport properties.