An IP (Internet Protocol) over WDM network is expected to be an infrastructure for the next-generation Internet by directly carrying IP packets on the WDM-based network. Among several architectures for IP over WDM networks, one promising way is to overlay a logical topology consisting of lightpaths over the physical WDM network so that IP packets are carried on the lightpaths. The conventional methods for designing the logical topology have been focusing on maximizing throughput of the traffic. However, when the WDM network is applied to IP, the end-to-end path provided by the logical topology of the WDM network is not suitable to IP since IP has its own metrics for route selection. In this paper, we propose a new heuristic algorithm to design a logical topology by considering the delay between nodes as an objective metric. This algorithm uses a non-bifurcated flow deviation to obtain a set of routes that IP packets are expected to traverse. Our proposal is then compared with conventional methods in terms of the average packet delays and throughput. It is shown that our method becomes effective when the number of wavelengths is a limited resource.