Unmanned Aerial Vehicles (UAVs) fleets are becoming more apparent in both military and civilian applications. However security of these systems still remains unsatisfactory if a strong adversary model with a high attack potential (i.e. the adversary has capabilities and knowledge to capture a UAV, to perform side-channel or fault injection or other physical, software or combined attacks in order to gain access to some secret data like cryptographic keys, mission plan, etc.) is considered. The aim of this position paper is to draw security requirements for this kind of adversaries and to propose theoretical solutions based on an embedded Secure Element (SE) that could help to accommodate these requirements. Finally, our proposal on how to use these SEs to secure Autonomous UAVs fleets is presented.