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In this paper, we present a model-based optimization approach for the design of multi-layer networks. The proposed framework is based on a series of increasingly abstract models – from a general technical system model to a problem specific mathematical model – which are used in a planning cycle to optimize the multi-layer networks. In a case study we show how central design questions for an IP-over-WDM network architecture can be answered using this approach. Based on reference networks from the German research project EIBONE, we investigate the influence of various planning parameters on the total design cost. This includes a comparison of point-to-point vs. transparent optical layer architectures, different traffic distributions, and the use of PoS vs. Ethernet interfaces.