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The National Aerospace Laboratory of Japan (NAL) and the Electronic Navigation Research Institute (ENRI) are researching a new aircraft operations concept, named NOCTARN, based on three-dimensional flight trajectories shared between aircraft and air traffic control (ATC) via digital data link and negotiated using Control Pilot Data Link Communications (CPDLC). It is proposed to incorporate a route modification function that would be invoked each time a route were assigned to modify the predefined trajectory based on wind conditions and aircraft performance in order to improve path tracking in strong wind while avoiding requiring maneuvers that could lead to loss of control. Route modification could also be used to assure separation between aircraft. This paper reports on the investigation by flight simulation into pilot acceptance of the NOCTARN system, the effects of route modification based on wind conditions and CPDLC operation upon manual flight control performance and pilot workload. The results indicate that modified routes successfully reduced path deviation and lowered pilot workload, and that the introduction of CPDLC procedures had no significant impact on manual flight control. Flight experiments further demonstrated that the proposed system and procedure is acceptable to the pilots.