Some embodiments of the invention provide a method for generating multi-layer topological routes in a region of a design layout. The method selects a net that has routable elements on a several interconnect layers. For the selected net, the method defines a topological route that connects the selected net's routable elements. The topological route includes a topological via that specifies the defined route's traversal from one interconnect layer to another interconnect layer, without having a coordinate within the region.