Path bundling consists in compounding multiple routes in a polygonal map to minimize connectivity in a network structure. Being closely related to the Steiner Tree Problem, yet with a different scope, path bundling aims at computing minimal trees while preserving network connectivity among origin-destination pairs to allow the joint transport of information, goods, and people. In this paper, we propose a method to tackle the path bundling problem in modular bipartite networks by using a two-layer optimization with a convex representation. Exhaustive computational experiments in diverse polygonal domains considering convex and non-convex geometry show the feasibility and the efficiency of the proposed approach, outperforming the state of the art in generating comparatively shorter trees, and improved scalability as a function of edges in bipartite networks.