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The use of micro unmanned aerial vehicles (UAVs) have gained a lot of interests especially for smart city applications due to their three- dimensional (3D) mobility and flexibility. Path planning is one of the most important UAV problems that needs to be addressed. In this paper, we focus on determining the optimal routes for a fleet of UAVs in urban cities that minimize the total arrival time of all UAV swarms while respecting their energy consumption constraints and avoiding the risk of collision. Through a mixed integer linear program, we develop a safe navigation framework for realistic 3D maps where charging stations are made available to recharge UAV batteries on their ways to destination. Our results investigate different scenarios for selected system parameters and illustrate different collision avoidance techniques followed by the UAVs.