In this paper we illustrate a new methodology for the design of fault-tolerant logical topologies in wavelength-routed optical networks exploiting wavelength division multiplexing, and supporting IP datagram flows. Our design approach generalizes the "design protection" concepts, and relies on the dynamic capabilities of IP to re-route datagrams when faults occur, thus achieving protection and restoration, and leading to high-performance cost-effective fault-tolerant logical topologies. In this paper, for the first time, we consider the resilience properties of the topology during the logical topology optimization process, thus extending the optimization of the network resilience also to the space of logical topologies. Numerical results clearly show that our approach outperforms previous ones, being able to obtain very effective survivable logical topologies with limited complexity.