The use of UAVs in military field is now widely diffused and the market of these machines is rapidly increasing. Not the same can be said for their use in civil field since the market for these machines is still practically nonexistent, despite we recognise the potential economical and operational considerable benefits that would result from their use in many activities requiring a control of the territory. The main obstacles that are currently preventing the use of these machines in civil field are related to issues of security and safety which actually make it impossible the use of military UAVs for civil matters. Security problems are related to the possibility that machines of this type can be used in attacks for undermining the security of citizens. Safety problems are related to the necessity to ensure the safety of the third overflown. As for conventional aircraft, the desired levels of safety could be achieved when they were available the appropriate certification codes that should be mainly related to the airworthiness, flight operations, maintenance, and air traffic control. Today, these codes are being developed, there are proposals and drafts, but none is officially approved. It's almost certain that the objective of these codes will be to ensure the probability of a catastrophic fall with a possibility of causing damage to persons or things overflown under 10-9 per hour of flight. This requirement makes it impossible to use military UAVs for civil matters as they are till now characterized by an attrition rate from 10 to 100 times higher than that of conventional civil aircrafts that respond to the aforesaid general safety requirement, even if it is referred to passengers. The UAVs for civil use should therefore be a new machine, designed since in project to respond to the stringent requirements of security and safety. Based on these considerations, since 1999 the Department of Aerospace Engineering (DIA) of the University of Pisa has set up a research, called SCAUT project (AUtomatic Control System of the Territory), focused on problems of safety and security, which currently oppose use of civil UVS (Unmanned Vehicle System) systems based on UAVs. This activity has led to the preliminary draft of a certificable UAV according with some drafts of certification codes currently available of a weight of 450 kg (SCAUT 450 project), the implementation of a flying model in scale 1:2 of maximum weight 60 kg (project SCAUT 60), a ground station for control of both UAVs and a test bench consisting of ground station + flight simulator for SCAUT 60 + SCAUT 60 used as iron bird (simulation in hardware in the loop ) used for the development of systems and studying the best techniques of interruption of flight without causing damage to the ground in case of serious breakdown on board. The conduct of such activities has shown that the main elements critical to the safety of the flight are the autopilot system, the navigation system and the mission management system and failure control. These systems with their management software constitute the onboard artificial intelligence replacing the human pilot. To them it is conventionally given the name of Flight Management System (FMS). Due to its characteristics, the FMS for use on certificable UAVs must stem together with the UAV project because it is intimately connected with it. In fact the main functions to be performed are closely related to the characteristics of the planned missions, the number and characteristics of the onboard systems, the levels of redundancy. Currently, certified or certificable UAVs don't exist for use in civil field and hence also their FMS systems are still to be defined as to their architecture and functionality. A simple FMS, implemented on PC/104, without redundancy to ensure the desired reliability requirements and able to handle some fundamental breakdowns, was developed to control the experimental SCAUT 60 model and gave the expected results in simulation tests, waiting for the flight tests.