This thesis presents a comprehensive framework and a study for trajectory optimization based on the patterned formation flying of the aircraft system as well as the maneuvers for deforming the configured and aligned aerial vehicles with safe mode criteria considerations while subjected to typical environmental requirements of aerial-flying zones. The elementary trajectory problem of a simple dynamical point-mass system of the aircraft is mathematically formulated and converted into a simulation version of mathematical programming as finite horizon planning and fixed arrival time planning strategies as an optimization problem. The methodology of the designed framework is mainly concerned with the safer path planning of the aircraft system with testing on all the probable feasibility and safety constraints to incorporate into a mathematical programming design of a collision-free and optimal trajectory characterization. The imperative notion is to create a configurational pattern of the aircraft system based on their creation of wingtip vortices. Flying the aircraft in formation lessen the fuel consumption as well as increase the time efficiency. The aircraft formation is arranged and optimized for safe trajectories during flight operations and for reduction of the carbon footprint of the whole system. Furthermore, deformation maneuvers are incorporated to complete the aircraft planning system by allowing the possibility of safely disassembling the formation for emergency breakout and exit sequences.