An intraoperative radiation therapy (IORT) system, comprising: a moveable cart adapted for selective transport; a robot arm assembly coupled to the cart, the robot arm assembly having at least one elongate arm (34, 36, 38) and at least five movement axes to increase positional flexibility and reach; at least one applicator adapted to be fixed near a target area of a patient, the at least one applicator having an elongate tube and an open endcap detachably mounted to one end of the tube, the at least one applicator defining an applicator axis; a treatment head coupled to the at least one elongate arm, the treatment head having a working end adapted to emit therapeutic beams towards the target area for radiation therapy, the treatment head adapted to be aligned with the applicator axis in a soft-docking process; at least one haptic control assembly coupled to the treatment head; a sensor array coupled to the working end of the treatment head, the sensor array having a plurality of sensors (112, 122) each with a given operational range, the sensors adapted to detect surfaces on the endcap and measure relative distance therebetween; the haptic control assembly configured to move the treatment head within detection range of the endcap on the applicator for a coarse alignment of the treatment head with the applicator axis in the soft-docking process; wherein the at least one haptic control assembly is configured to move the sensor array within sensing range of the endcap for the coarse alignment; a controller for controlling operation of the IORT system; and a control panel associated with the controller and having a plurality of switches (151, 152, 153, 154, 155, 156, 157) for controlling movements of the cart, the robot arm assembly, and the treatment head, wherein the control panel is configured to enable autonomous fine alignment of the treatment head based on sensed data from the sensor array after the coarse alignment. a moveable cart adapted for selective transport; a robot arm assembly coupled to the cart, the robot arm assembly having at least one elongate arm (34, 36, 38) and at least five movement axes to increase positional flexibility and reach; at least one applicator adapted to be fixed near a target area of a patient, the at least one applicator having an elongate tube and an open endcap detachably mounted to one end of the tube, the at least one applicator defining an applicator axis; a treatment head coupled to the at least one elongate arm, the treatment head having a working end adapted to emit therapeutic beams towards the target area for radiation therapy, the treatment head adapted to be aligned with the applicator axis in a soft-docking process; at least one haptic control assembly coupled to the treatment head; a sensor array coupled to the working end of the treatment head, the sensor array having a plurality of sensors (112, 122) each with a given operational range, the sensors adapted to detect surfaces on the endcap and measure relative distance therebetween; the haptic control assembly configured to move the treatment head within detection range of the endcap on the applicator for a coarse alignment of the treatment head with the applicator axis in the soft-docking process; wherein the at least one haptic control assembly is configured to move the sensor array within sensing range of the endcap for the coarse alignment; a controller for controlling operation of the IORT system; and a control panel associated with the controller and having a plurality of switches (151, 152, 153, 154, 155, 156, 157) for controlling movements of the cart, the robot arm assembly, and the treatment head, wherein the control panel is configured to enable autonomous fine alignment of the treatment head based on sensed data from the sensor array after the coarse alignment.