Nowadays, reverse engineering is widely spread in the manufacturing industry. The need of shorter development cycles has led to the identification of social and economic issues related to reverse engineering. The integration of a reverse engineering solution in a PLM context represents a good solution in order to shorten the development cycles, especially when it is automated. In this paper we present the issues identified in the context of METIS, a French national project aiming to provide a software solution for reconstructing large and complex mechanical assemblies and systems, through a global reverse engineering methodology combined with a knowledge management approach, and using heterogeneous data as inputs.