We have investigated the 2x12 o symmetric grain boundary of (001) oriented bicrystalline silicon substrates for high-T c superconductor applications using scanning focused ion beam (FIB) and electron beam (SEM). We successfully used the focused ion beam to detect and to mark the grain boundary and hence, to increase the accuracy of positioning the Josephson device with respect to the grain boundary of the silicon substrate. Both imaging methods have been compared using channeling effects of focused ion and electron beams in a dual beam system.