Radiation induced clustering affects the mechanical properties, that is the ductile to brittle transition temperature (DBTT), of reactor pressure vessel (RPV) steel of nuclear power plants. The combination of low Cu and high Ni used in some RPV welds is known to further enhance the DBTT shift during long time operation. In this study, RPV weld samples containing 0.04 at% Cu and 1.6 at% Ni were irradiated to 2.0 and 6.4×1023 n/m2 in the Halden test reactor. Atom probe tomography (APT) was applied to study clustering of Ni, Mn, Si, and Cu. As the clusters are in the nanometer-range, APT is a very suitable technique for this type of study. From APT analyses information about size distribution, number density, and composition of the clusters can be obtained. However, the quantification of these attributes is not trivial. The maximum separation method (MSM) has been used to characterize the clusters and a detailed study about the influence of the choice of MSM cluster parameters, primarily on the cluster number density, has been undertaken.