The ideal picture of a near-perfect 3D microscope often presented regarding Atom Probe Tomography faces several issues. These issues degrade the metrological performance of the instrument and find their roots in the phenomena acting at the atomic to the mesoscopic level in the vicinity of the surface of a field emitter. From the field evaporation process at the atomic scale, to the macroscopic scale of the instrument, the path to model the imaging process and to develop more accurate and reliable reconstruction algorithms is not a single lane road. This paper focused on the numerical methods used to understand, treat, and potentially heal imaging issues commonly affecting the data in atom probe experiments. A lot of room for improvement exists in solving accuracy problems observed in complex materials by means of purely electrostatic models describing the image formation in a classical approach. Looking at the sample at the atomic scale, the phenomena perturbing the imaging process are subtle. An examination of atomic scale modifications of the sample surface in the presence of a high surface electric field is therefore mandatory.Atomic scale molecular dynamic models integrating the influence of the high surface electric are being developed with this aim. It is also demonstrated that the complex behavior of atoms and molecules in high fields, and consequences on collected data, can be understood through the use of accurate ab-initio models modified to include the impact of the extreme surface electric field.The capability to correlate the physical properties of materials to the local three dimensional distribution of atoms is nowadays crucial in designing new and improved materials and devices. When designing nanostructured materials, the dream is to be able to catch with the highest metrological performance a snapshot of the region of interest. Being able to identify structural and elemental information with 3D details on the single-atom level could transform the understanding of the relationship between structure (e.g. composition, defects, crystallography) and properties (e.g. magnetic, electric, photonic, or mechanical properties for instance) at the most fundamental level. This approach is explored using the atom probe tomography instrument (APT). This instrument is indeed unique in the world of nano-analysis tools, for its ability to provide, after analysis of a volume of interest in the material, a 3D map of atom positions, with atoms labelled by their elemental identities [1,2,3,4].By wandering between the static positions of atoms present in an APT dataset, the instrument's user often feels that the three dimensional image is a snapshot of the specimen that was left unharmed by the analysis process. This feeling is obviously an illusion. At the APT specimen level, i.e. a sharply pointed needle (called the tip), the imaging process utilizes extremely intense physical mechanisms on the surface and sub-surface of the materials. A strong electric voltage generates locally a huge surface electric field (sever...