The gas field ion source (GFIS) is able to generate tightly focused ion beams, which can be used to image or modify a specimen. Among the beam species, helium offers extremely high resolution, however, low sputter yield and sub-surface bubble formation are limiting factors in some applications. Therefore, heavier ions such as neon or nitrogen are used as well. In addition to being a suitable choice for lithographic mask editing, secondary electron (SE) generation by nitrogen beams has been recently shown to be affected by certain types of samples, providing additional contrast compared to helium ions. Here, we report our progress on the study of SE imaging differences between the nitrogen ion microscopy (N2IM) and helium ion microscopy (HIM). SE images of two nano-patterned samples comprising insulator, metal and carbon regions have been imaged by nitrogen and helium ions in two fundamentally different GFIS microscopes. The results corroborate previous reports of significant contrast differences in certain samples caused by the different ion species.