Minimal trees in polygonal maps aim at minimizing the connectivity in a network while avoiding obstacle collision. Being closely related to the Steiner Tree Problem, yet with a different scope, minimal trees aim at connecting origin-destination pairs, given in a bipartite network, to allow the joint transport of information, goods, resources and people. In this paper, we propose a method to tackle the bundling problem of minimal trees in modular bipartite networks by using a two-layer optimization based on Differential Evolution with a convex representation of coordinates. Our computational experiments in polygonal domains considering both convex and non-convex geometry show the feasibility and the efficiency of the proposed approach.