Among all the microscopy or tomographic instruments, atom probe tomography occupies a singular position. The information extracted from the analysis is indeed reduced to the discrete positions of atoms (and the elemental nature of these atoms) contained in a small and defined volume of matter. These positions are deduced from the ordered list of impact coordinates of ions resulting from the process of field evaporation of the sample. This chapter describes the basic principles of the reconstruction of the three-dimensional images in atom probe. Starting from the basic hypotheses of the emission process, the general protocol for atom probe reconstruction is detailed. This understanding is of fundamental importance to evaluate the metrology performances of the instrument, in terms of spatial accuracy and precision. In addition, the possible artifacts of the technique in the analysis of different class of materials from pure metals to complex heterogeneous nanomaterials will be presented. The role of the modeling approach and the current reconstruction methods used to overcome classical shortcomings will be detailed. A selection of exercises is proposed at the end of the chapter.