This paper studies the trajectory planning problem for multiple aircraft with logical constraints in disjunctive form which arise in modeling passage through waypoints, distance-based and time-based separation constraints, decision-making processes, conflict resolution policies, no-fly zones, or obstacle or storm avoidance. Enforcing separation between aircraft, passage through waypoints, and obstacle avoidance is especially demanding in terms of modeling efforts. Indeed, in general, separation constraints require the introduction of auxiliary integer variables in the model; for passage constraints, a multiphase optimal control approach is used, and for obstacle avoidance constraints, geometric approximations of the obstacles are introduced. Multiple phases increase model complexity, and the presence of integer variables in the model has the drawback of combinatorial complexity of the corresponding mixed-integer optimal control problem. In this paper, an embedding approach is employed to transform logical constraints in disjunctive form into inequality and equality constraints which involve only continuous auxiliary variables. In this way, the optimal control problem with logical constraints is converted into a smooth optimal control problem which is solved using traditional techniques, thereby reducing the computational complexity of finding the solution. The effectiveness of the approach is demonstrated through several numerical experiments by computing the optimal trajectories of multiple aircraft in converging and intersecting arrival routes with time-based separation constraints, distance-based separation constraints, and operational constraints.