In many cases in experimental science, it is true that the instrument interface becomes a limiting factor in the efficacy of carrying out unusual experiments, or prevents the complete understanding of the acquired data. We are developing an advanced interface for Scanning Probe Microscopy (SPM) which allows intuitive rendering of datasets and natural instrument control, all in real-time. The interface, called the nanoManipulator, combines a high performance graphics engine for real-time data rendering with a haptic interface which places the human operator directly into the “feedback loop” that controls surface manipulations. In practice, the user holds a stylus in hand. By moving the stylus laterally, the user directs the movement of the SPM tip across the sample. The haptic interface enables the user to “feel” the surface by forcing the stylus to move up and down in response to the surface topography.