We are developing a cooperatively-controlled robot system in which a clinician and robot share control of a 3D ultrasound (US) probe. The goals of the system are to provide guidance for patient setup and real-time target monitoring during fractionated radiotherapy. Currently, there is limited use of real-time US image feedback during radiotherapy for lower abdominal organs and it has not yet been clinically applied for upper abdominal organs. One challenge is that placing an US probe on the patient produces tissue deformation around the target organ, leading to displacement of the target. Our solution is to perform treatment planning on the deformed organ and then to reproduce this deformation during radiotherapy. We therefore introduce a robot system to hold the US probe on the patient. In order to create a consistent deformation, the system records the robot position, contact force, and reference US image during simulation and then introduces virtual constraints (soft virtual fixtures) to guide the clinician to correctly place the probe during the fractionated treatments. Because the robot is under-actuated (5 motorized and 6 passive degrees-of-freedom), the guidance also involves a graphical user interface (adjustment GUI) to achieve the desired probe orientation. This paper presents the integrated system, a proposed clinical workflow, the results of an initial in-vivo canine study with a 3-DOF robot, and the results of phantom experiments with an improved 5-DOF robotic system. The results suggest that the guidance may enable the clinician to more consistently and accurately place the US probe.