In this paper we will present a solution for automatic design rule checking (DRC) and layout versus schematic comparison (LVS) of 2.5D/3D systems, which enables an early check of subcomponents as well as whole system checks. The advantage of our approach is the unique data handling for different DRC and LVS runs, which allows the automatic derivation of partial design data from one single data base. Such an approach is essential for industrial driven designs of 2.5/3D systems. Otherwise, there is a high risk of mistakes related to data conversion and versioning problems. Such data handling issues can result in erroneous designs and cost extensive redesigns