System and methods are disclosed for augmenting a synthesized NoC, with data that guides a physical implementation of the NoC topology in a way that coincides with the topology synthesis result and reduces timing violations in the final physical design. The system generates physical implementation guidance, which is during physical implementation of the synthesized NoC. The system inserts a link as a pipeline placeholder and a minimum set of created module regions are assigned to a specific link of the topology. Each route has a new link and corresponding module region inserted into the physical path.