The future of flight is unmanned aircraft. The use of remotely-piloted aircraft for military operations is now familiar to us. There are also seen to be benefits for use of Unmanned Aircraft Systems (UAS) for civil use. The method of controlling unmanned aircraft using remote pilots is seen to be very limiting. Therefore the future of this technology needs autonomous control and intelligence, which bring additional safety concerns. The ASTRAEA (Autonomous Systems Technology Related Airborne Evaluation and Assessment) programme was set up to generate and aid this development. Safety of civil unmanned flight is a focal point of this programme which recognises that there are significant regulatory issues to be overcome. Without a physical product to certify it is difficult for stakeholders to commit to definitive solutions to such issues. A programme named Virtual Certification was devised as a way to address them. Regulation and duty-of-care considerations would require a large programme of safety activities for any autonomous UAS that was intended to fly in civil airspace also occupied by manned aircraft. These activities require appropriate hazard analyses. Fault tree analysis is one of the techniques specified by the existing civil aviation standards and is a suitable graphical means of communicating how safety hazards have been ad-dressed in a system or subsystem. It is generally accepted that to operate a UAS in non-segregated airspace a comprehensive separation approach is needed to avoid mid-air collisions (and also near-misses). Such an approach requires a Sense and Avoid system on the airborne part of the UAS, the Unmanned Aircraft (UA). It is generally regarded that this system would need to work with a degree of autonomy in order to detect other objects which it may potentially collide with. To certify any UAS it is necessary to demonstrate that the separation approach, including the Sense and Avoid system, is safe to use. A fault tree analysis for doing so is presented here as well as an overview on autonomy and the ASTRAEA Virtual certification Programme.