The objective of the paper is to present an overall design methodology based on the finite element method (FEM), where the focus is on the relation between the controller design and the multi-physics structure, consisting of the passive base structure, the actuators, the sensors and also the control electronics. First, it is shown how such an overall virtual computer model can be generated and applied to design smart structures and to study the behavior of the structures under different operating conditions taking into account also disturbances, model uncertainties, etc. As a reference example a smart plate structure is used to discuss different design versions and controller approaches in detail. Then two industrial applications are briefly mentioned, where our approach was used to design the structures based on an overall virtual computer model.