For critical civil and military missions, the Unmanned Aerial Vehicles (UAVs) are continuously attracting attention. UAVs should collect data for a defined area with a variety of sensors. When these UAVs are operating in swarm formation, the observation area could be increased and it would also be possible to deal with a loss of a UAV. The big amount of data produced by the UAVs requires high date rate connectivity, therefore the free space optical (FSO) communication is suitable. When using FSO links some important issues need be considered, the beam attenuation due the atmosphere on one side and the alignment of the FSO units on the other side. The alignment raises technical challenges in tracking and acquisition. The combination of UAVs with the FSO communication is an interesting investigative scenario and some of the important aspects of this ambitious design are the main focus of this paper.