A generic process for simulation-based system identification for civil engineering problems is presented. It is iterative and contains a feedback loop for the continuous refinement of the system, taking into account the sensor values of the real object. The process was implemented in a generic workflow engine that can be integrated into software systems and adapted to specific application scenarios. An exemplary implementation in the context of a cyber-physical system for dynamic adaptation of production processes shows the feasibility and the advantages of the developed concept.