Nano-particles are of great interest in fundamental and applied research. However, their accurate visualization is often difficult and the interpretation of the obtained images can be complicated. We present a comparative scanning electron microscopy and helium ion microscopy study of cetyltrimethylammonium-bromide (CTAB) coated gold nano-rods. Using both methods we show how the gold core as well as the surrounding thin CTAB shell can selectively be visualized. This allows for a quantitative determination of the dimensions of the gold core or the CTAB shell. The obtained CTAB shell thickness of 1.0 nm–1.5 nm is in excellent agreement with earlier results using more demanding and reciprocal space techniques.