Aircraft en-route flight planning is one of the major challenges for Air Traffic Control operations. Poor planning results in undesirable congestion in the air-traffic network, causing major economic losses for both airline companies and the public. Furthermore, heavy congestion generates flight safety risks due to increased possibility of mid-air conflict. To address these problems, this paper introduces a non-time segmented en-route flight plan formulation with rerouting options for aircrafts in a 3-dimensional (3D) capacitated airspace. Novelty of the proposed mathematical model is the non-time segmented formulation that captures exact arrival and departure times to/from each air-sector. The proposed formulation also incorporates sector capacity changes due to changing weather conditions during planning horizon. Moreover, the speed dependent fuel consumption rate is introduced as a factor in thezone-based air traffic flow management problem. In order to handle the problem sizes similar to those in real-world cases, we proposed a sequential solution heuristics. The performance of the sequential solution method is demonstrated through various test cases.