Focused ion beam specimen preparation has been used for NiTi samples and SrTiO3/SrRuO3 multilayers with prevention of surface amorphization and Ga implantation by a 2-kV cleaning procedure. Transmission electron microscopy techniques show that the samples are of high quality with a controlled thickness over large scales. Furthermore, preferential thinning effects in multicompounds are avoided, which is important when analytical transmission electron microscopy measurements need to be interpreted in a quantitative manner. The results are compared to similar measurements acquired for samples obtained using conventional preparation techniques such as electropolishing for alloys and ion milling for oxides.