This paper describes the development of an intelligent automated control system of a robot manipulatorfor plasma treatment of medical implants with complex shapes. The two-layer coatings from the Ti wire and hydroxyapatite powders are applied on the surface of Ti medical implants by microplasma spraying to increase the biocompatibility of implants. The coating process requires precise control of a number of parameters, particularly the plasma spray distance and plasma jet traverse velocity. Thus, the development of the robotic plasma surface treatment involves automated path planning. The key idea of the proposed intelligent automatic control system is the use of data of preliminary three-dimensional (3D) scanning of the processed implant by the robot manipulator. The segmentation algorithm of the point cloud from laser scanning of the surface is developed. This methodology is suitable for robotic 3D scanning systems with both non-contact laser distance sensors and video cameras, used in additive manufacturing and medicine.