Transmission electron microscopy studies of localized Ge and GeSi surface nanostructures in the form of nanowires on a Si substrate were performed using a novel specimen preparation scheme assisted by a focused ion beam (FIB). The Ge nanowires/Si and GeSi nanowires/Si were fabricated in a lift-off process using e-beam lithography and a pulsed UV laser induced epitaxy process, respectively. By using a Pt/Au-Pd/C multilayer protection structure over the area of interest and a FIB marking technique, specimens of lattice imaging quality have been consistently obtained in which all features of interest were preserved. Multilayer protection structures of Pt/C and Pt/Au-Pd/spin-on-glass were also investigated. The versatile sample preparation procedure is applicable to a wide variety of surface structures other than the kind used in this work.