The problem of physical design automation is a difficult problem due to the huge number of devices, and physical constraints to be met. The Model-Driven Engineering (MDE) approach aims to tackle the complexity of software development using a high level method based on models and transformations. While this approach is used for High-Level circuit synthesis there is no work reported on the lower part of the circuit design automation flow, namely the physical-design automation. In this work, we use the MDE approach to model the physical synthesis process with a focus mainly on reconfigurable architectures. We present a model for island style FPGAs along with the transformations needed in the case of the physical synthesis. The main result of this work is to show the feasibility of the MDE approach for the physical design automation problem, and we argue that this methodology enables orthogonal composition of the architecture / algorithms / application design space, that enables incremental exploration based on quantitative evaluations.