The finite elements method (FEM) is a useful tool for the analysis of the strain state of semiconductor heterostructures. It has been used for the prediction of the nucleation sites of stacked quantum dots (QDs), but often using either simulated data of the atom positions or two-dimensional experimental data, in such a way that it is difficult to assess the validity of the predictions. In this work, we assess the validity of the FEM method for the prediction of stacked QD nucleation sites using three-dimensional experimental data obtained by atom probe tomography (APT). This also allows us to compare the simulation results with the one obtained experimentally. Our analysis demonstrates that FEM and APT constitute a good combination to resolve strain-stress problems of epitaxial semiconductor structures.