Elemental distributions in a magnetic multilayer system with the structure Si substrate/Ta/NiFe/Ru/CoFeB/Ru/NiFe were studied using atom probe tomography (APT) along different analysis directions. The distributions of Ru and B atoms, which require a high evaporation field, were strongly influenced by the APT analysis direction. In particular, B in the CoFeB layer appeared near the interface with the lower Ru layer when the analysis was anti-parallel to the film growth direction, while B atoms were observed at the other side of the CoFeB layer when the analysis was parallel to the film growth direction. Moreover, when the analysis was perpendicular to the film growth direction, a homogenous distribution of B atoms was found within the CoFeB layer. Owing to this B behavior, the underlying Ru layer was affected in both of these analysis directions. In APT measurements of such a multilayer system composed of a stack of different evaporation field materials, evaluation of the elemental distribution around interfaces should be performed from more than one analysis direction.