To meet the ever-increasing requirements of onchip communication, the trend is towards wavelength-routed optical networks-on-chip (WRONoCs), which support high-speed communication with low power. A typical WRONoC design flow consists of two consecutive steps: topological design and physical design. Current physical design tools interpret the input topology as a pure logic scheme and perform placement and routing for all network components from scratch. Due to the large design complexity and the layout constraints, additional waveguide crossings in the synthesized layouts are hardly avoidable, which results in an increase in insertion loss and crosstalk noise and thus degrades the network performance. In this work, we propose a physical design tool, ToPro, which retains the interconnection among the optical switching elements by projecting the structure of a WRONoC topology onto the physical plane, and focuses on the waveguide routing to the IP-cores. To avoid the increase in insertion loss and crosstalk noise, ToPro removes the extra crossings and long detours of waveguides by changing the routing order of nets. The experimental results demonstrate the superiority of ToPro in time-and energy-efficiency. For example, compared to a state-of-the-art design automation tool, ToPro synthesizes a network with 16 IP-cores with a 17% reduction on the worst-case insertion loss and decreases the synthesis time from more than six days to less than one second.