This work contributes to the understanding of focused ion beam (FIB) technology for polymers. The conditions of treatment are varied, in particular by etching under 'dry' ultra-high vacuum conditions or in the presence of water vapour. For a glassy epoxy network, the changes in chemistry and morphology are characterised. Energy-dispersive X-ray analysis reveals that gallium is always implanted in the epoxy but the content is higher in the case of 'dry' FIB milling. According to attenuated total reflection infrared micro-spectroscopy, new chemical structures form in the surface region of the epoxy during FIB milling with or without water vapour. Scanning electron microscopy and scanning force microscopy were used to image the topography of the etched epoxy surfaces. Quite smooth surfaces result under 'dry' etching conditions. In the presence of water vapour, rough surfaces with a sub-micrometre globular morphology are obtained. This is an indication of the heterogeneous morphology of the epoxy polymer. As compared to 'dry' conditions, the introduction of water vapour during FIB milling increases the milling yield significantly. As a result, the FIB treatment changes the chemistry and the structure of the epoxy network not only at the very surface but also in some significant surface layer of the sample. It can be expected that such a modified zone will also form on other cross-linked polymers.