Accuracy of atom probe tomography measurements is strongly degraded by the presence of phases that have different evaporation fields. In particular, when there are perpendicular interfaces to the tip axis in the specimen, layers thicknesses are systematically biased and the resolution is degraded near the interfaces. Based on an analytical model of field evaporated emitter end-form, a new algorithm dedicated to the 3D reconstruction of multilayered samples was developed. Simulations of field evaporation of bilayer were performed to evaluate the effectiveness of the new algorithm. Compared to the standard state-of-the-art reconstruction methods, the present approach provides much more accurate analyzed volume, and the resolution is clearly improved near the interface. The ability of the algorithm to handle experimental data was also demonstrated. It is shown that the standard algorithm applied to the same data can commit an error on the layers thicknesses up to a factor 2. This new method is not constrained by the classical hemispherical specimen shape assumption.