In this article, we report silicon-based multilayered nanometer-size wires for vertical metal oxide semiconductor held effect transistor (MOSFET) and the ohmic contact of gallium nitride (GaN) field effect transistor (FET) were milled to produce trenches with a micron-scale rectangular area for a subsequent inspection by the field emission scanning electron microscope (FESEM). The cross-sectioning view by the FESEM enabled the investigation of individual film thickness and morphology as well as a depth profiling of elements by a subsequent Auger analysis. Monte Carlo simulation was done to estimate the penetration range of gallium ions into silicon and GaN at high energy.