A study to analyse beam damage, image quality and edge contrast in the helium ion microscope (HIM) has been undertaken. The sample investigated was graphene. Raman spectroscopy was used to quantify the disorder that can be introduced into the graphene as a function of helium ion dose. The effects of the dose on both freestanding and supported graphene were compared. These doses were then correlated directly to image quality by imaging graphene flakes at high magnification. It was found that a high magnification image with a good signal to noise ratio will introduce very significant sample damage. A safe imaging dose of the order of 1013 He+ cm-2 was established, with both graphene samples becoming highly defective at doses over 5 × 1014 He+ cm-2. The edge contrast of a freestanding graphene flake imaged in the HIM was then compared with the contrast of the same flake observed in a scanning electron microscope and a transmission electron microscope. Very strong edge sensitivity was observed in the HIM. This enhanced edge sensitivity over the other techniques investigated makes the HIM a powerful nanoscale dimensional metrology tool, with the capability of both fabricating and imaging features with sub-nanometre resolution. © 2013 IOP Publishing Ltd.