The helium ion microscope (HeIM) holds immense promise for nano-engineering and imaging with scope for in-situ chemical analysis. Here we will examine the potential of secondary electron hyperspectral imaging (SEHI) as a new route to exploring chemical variations in both two and three dimensions. We present a range of early applications in the context of image interpretation in wider materials science and process control in ion beam-based nano-engineering. Necessary steps for SEHI in the HeIM to evolve into a reliable technique which can be fully embedded into nano-engineering workflows are considered.