Micromanipulation tools are not yet commonly used in the industry or in the research due to the lack of natural and intuitive human-computer interfaces. This work proposes a vision based approach using a Kinect RGB-Depth sensor to provide a ”metaphor-free” interface. An intention prediction approach is proposed, based on a cognitive science computational model, to allow a more natural interaction without any prior instructions. This model is compared to a vision based gesture recognition approach in terms of naturalness and intuitiveness. It shows an improvement in user performance in terms of duration and success of the task, and a qualitative preference for the proposed approach evaluated by a user survey.