This dissertation addresses the important issue of the methodology of transferring aircraft from regions of airspace where "Autonomous Aircraft Operations" (AAO) is performed to regions of conventionally Managed Airspace (MAS), and vice versa. This transfer is a key component to the feasibility of the AAO concept in the future Air Traffic Management (ATM) system. The term "Autonomous Aircraft Operations" (AAO) is used to describe a regime of flight where the problems of today's restrictive airspace structure are overcome by allowing pilots of suitably equipped aircraft the freedom to establish their own flight path, speed and altitude in real time. A consequence of this freedom is that responsibility for the maintenance of safe separation is delegated to the aircraft alone. The benefit of AAO is the potential to improve the capacity of airspace and efficiency of flight operations in regions of airspace with no radar-based air traffic control coverage. By allowing pilots to choose their own flight parameters, they will be able to follow a flight plan that matches the most efficient and economical route for their aircraft, thus reducing fuel consumption and the emission of pollution. Aircraft will be able to meet more accurately their planned times of departure and arrival, and minimise en-route delays. Such factors will result in reduced costs to airlines and ultimately, their customers. In short, the four principles on which future ATM systems are designed (safety, capacity, efficiency and environmental) are met by AAO. Airspace in which AAO may operate is expressed as "Free Flight" Airspace (FFAS). In a mixed-mode environment where areas of FFAS will border areas of MAS, Autonomous Aircraft must ideally be allowed to pass between the two airspace regions without deviation or significant delay while avoiding potential conflict with other aircraft. It is proposed that this desired condition can be met by the adequate scheduling of Autonomous Aircraft at FFAS entry or exit points. The study reported in this dissertation principally investigated the lateral transfer from FFAS to MAS (both en-route and terminal area airspace). For this, a Transfer Management Tool (T-MAT) has been developed where work has centred around the novel concept of a dynamically-sized transfer zone. This is an extension into FFAS of MAS where aircraft will be instructed to adjust their intended speed schedule thus enabling them to meet a scheduled MAS entry time. The method uses the Analytic Hierarchy Process (AHP) allowing transfer zone trajectories to be selected according to aircraft operators' preferred procedures. In addition, this research also develops three separate scheduling algorithms for FFAS to en-route airspace transfer. The first seeks to ensure the safe separation of two aircraft in-trail after entering en-route airspace, the second seeks to solve conflict at fixed airway crossing points in en-route airspace, while the third seeks to manage air traffic controller workload in en-route airspace sectors that border FFAS. For FFAS to terminal area transfer, the use of scheduling systems such as CTAS or COMPAS is proposed. To illustrate the functionality and capabilities of the proposed algorithms, the dissertation concludes with selected testing based on Monte Carlo simulation.