In this paper, we present a complete pipeline for positioning a feature point of a soft object to a desired 3D position, by acting on a different manipulation point using a robotic manipulator. For that purpose, the analytic relation between the feature point displacement and the robot motion is derived using a coarse mass-spring model (MSM), while taking into consideration the propagation delay introduced by a MSM. From this modeling step, a novel closed-loop controller is designed for performing the positioning task. To get rid of the model approximations, the object is tracked in realtime using a RGB-D sensor, thus allowing to correct on-line any drift between the object and its model. Our model-based and vision-based controller is validated in real experiments for two different soft objects and the results show promising performance in terms of accuracy, efficiency and robustness.