Along with fast progress in robot technologies, robots nowadays are able to tackle complex tasks in organized environments, like factories. However, when they are introduced to human societies, the uncertain and unstructured environments pose much challenge for them to work alone. As detailed programming to deal with all possible scenarios is way too time-consuming, one alternate is to let the human execute the manipulation, but with an effective manipulation system. In this paper, we thus propose such a manipulation system that can achieve natural and efficient governing in real-time. The target robot manipulator is chosen to be with multiple degrees of freedom (DOF) and positioncontrolled for being popular and versatile. We adopt a force-reflection joystick as its manipulative device, which provides haptic feedback and mutual interaction. We also develop a set of virtual tools, a virtual spring, and a virtual bumper to assist the user when executing 3D applications with requirements on both position and orientation. For demonstration, the proposed manipulation system is applied for the tasks of contour following and also screw fastening.