We have formulated and examined an autonomous organization system for a transportationnetwork system. In this paper, we have considered costs not only for traversing the network but alsofor maintaining some routes on it. We assume that a working agent utilizes pheromone like items fornavigating them. We have formulated a traversing cost of a route by considering the density of theitems, which reflects the density of agents using the route. An agent arranges its route iteratively,then a whole network converges a state. Because the cost function becomes nonlinear equation,the topology of the emerged network depends on the resource of the system, the population of theagents. The results show that the proposed algorithm can change a transportation network into afeasible topology with a minimum traversing cost and the properties of a small world network.