This paper presents the operational scenario of the CANYVAL-X (Cubesat Astronomy by NASA and Yonsei using Virtual telescope ALignment eXperiment) mission and along with the resulting lessons learned from the early operation. The objective of this demonstration mission is to verify a vision alignment system with two CubeSats in low Earth orbit. The CubeSats were launched on 12 January 2018 at Sriharikota launch site by PSLV-C40. CubeSat Yonsei team designed the operational scenario and developed automatic communication programs to manage normal CubeSat operation. After 43 days from the launch, the first beacon signal from the 2U CubeSat was received at the ground station in Yonsei University. The ping between the CubeSat and the ground station was used to check the FM communication. Repetitive attempt was made to download the log file from the first reception of the beacon signal. Currently, telecommand and telemetry are not carried out successively since the FM communication of the ground station is acting abnormal. From these experience during the early operation of CANYVAL-X, CubeSat Yonsei team learned valuable lessons for the future mission such as the beacon carriage and the storage management design strategy.