A numerical model has been developed to simulate images obtained from the three-dimensional atom probe. This model was used to simulate the artefacts commonly observed in two-phase materials. This model takes into account the dynamic evolution of the atomic-scale shape of the specimen during field evaporation. This article reviews the model and its applications to some specific cases. Local magnification effects were studied as a function of the size, the shape, and the orientation of precipitated phases embedded in the matrix. Small precipitates produce large aberrations in good agreement with experiments. The magnification from such precipitates, as measured from the simulation, is only found to match the theoretical value for mesoscopic scale precipitates (size similar to the specimen size). Orientation effects are also observed in excellent agreement with experiments. The measured thickness of a grain-boundary-segregated film in the simulation is found to decrease with the angle between the normal to the grain boundary and the tip axis. Depth scaling artefacts caused by variation in the evaporation field of atoms in multilayer structures were successfully simulated and again showed good agreement with effects observed experimentally.