Field ion microscopy (FIM) was the first technique to image individual atoms on the surface of a material. By a careful control of the field evaporation of surface atoms, the bulk of the material is exposed, and, through digital processing of a sequence of micrographs, an atomically-resolved three-dimensional reconstruction can be achieved. 3DFIM is particularly suited to the direct observation of crystalline defects that underpin the physical properties of materials: vacancies and vacancy clusters, interstitials, dislocations, or grain boundaries. Yet, further developments of 3DFIM are necessary to turn it into a routines technique. Here, we introduce first a protocol for 3DFIM image processing and subsequent tomographic reconstruction. Second, we propose a numerical model enabling simulation of the FIM imaging process. The model combines the meshless algorithm for field evaporation proposed by Rolland et al. (Robin–Rolland Model, or RRM) with fundamental aspects of the field ionization process of the gas image involved in FIM. The proposed model enables the simulation of imaging artefacts that are induced by non-regular field evaporation and by the disturbed electric field distribution near atomic defects. Our model enables more precise interpretation of 3DFIM characterization of structural defects.