In this study, the Vehicle Routing Problem Pickup and Delivery with Time Windows (VRPPDTW) is considered. The VRPPDTW problem is seen in many practical applications such as logistics, distribution and transportation. Firstly, a new model of the very close to real-life problem is defined. Secondly, a novel heuristic algorithm with a new objective function is proposed to solve the daily macro routing problem with time windows. The method proposed to solve VRPPDTW problem is an extended version of a nature-inspired algorithm called Heuristic Bubble Algorithm (HBA). In order to express the benefit of using extended HBA, five case studies are discussed using RouteArt. The obtained results provide promising solutions in terms of average vehicle load efficiency, average service time, and total waiting time of the vehicle.