Virtual reality (VR) technology plays a significant role in many biomedical applications. These VR scenarios increase the valuable experience of tasks requiring great accuracy with human subjects. Unfortunately, commercial VR controllers have large positioning errors in a micro-manipulation task. Here, we propose a VR-based framework along with a sensor fusion algorithm to improve the microposition tracking performance of a microsurgical tool. To the best of our knowledge, this is the first application of Kalman filter in a millimeter scale VR environment, by using the position data between the VR controller and an inertial measuring device. This study builds and tests two cases: (1) without sensor fusion tracking and (2) location tracking with active sensor fusion. The static and dynamic experiments demonstrate that the Kalman filter can provide greater precision during micro-manipulation in small scale VR scenarios.