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In modern transport networks, IP routers and carrier Ethernet transport switches operate on top of optical networks providing huge transport capacities gained with wavelength division multiplex systems. The optical layer offers a flexible connectivity service to the packet layer and can establish direct connections between any pair of IP routers and Ethernet switches by light paths that transparently bypass routers and switches within the optical domain at intermediate sites. Thus the network topology seen by the packet layer becomes a major design parameter. Transit traffic can very flexibly be handed over to the packet layer at intermediate sites or transparently bypassed in the optical layer, whatever is more cost-effective. Remote reconfigurable optical cross connects even enable the topology of the packet layer to be adapted dynamically. In cooperation with Swisscom, Switzerland's leading telecoms provider, we investigated cost minimizing packet layer topologies of multi-layer transport networks. We applied mixed integer programming to calculate cost minimizing solutions for a reference network provided by Swisscom. The study revealed that the topology of a cost optimized IP layer depends on the traffic load, on the available data rates, and on the cost ratios of interfaces cards with different data rates. As a result the topology of the IP layer should be a dynamic network design parameter in order to maintain cost minimized transport networks.