Atom probe tomography (APT) is a tool for detailed chemical composition analysis of advanced structural material nanostructure. The use of different Atomic Probe Tomography (APT) devices requires a certification of these setups prior to conducting research. In this paper a method of comparing APT setups in order to evaluate the influence of the overall system configuration on the accuracy of obtained data is proposed. The collected data comparison is presented for the aluminum alloy Al–3.3Cu–2.5Mn–0.5Zr and structural steel 16Kh12МVSFBR gathered on the APPLE-3D (“PAZL-3D”) setup and on the new ATLAS (“ATLAZ”) unit, created through upgrading the ECOTAP. Comparison of the results confirms the feasibility of carrying out research of the same material on similar setups without significant distortion of the data under its analysis and interpretation.