In this study we describe the development of a six Degree of Freedom (6 DOF) pose estimation model of a tracked object and 3D user interface using stereo vision and Infra-Red (IR) cameras in the Matlab/Simulink and C# environments. The raw coordinate values of the IR light sources located on the tracked object are detected, digitized and Bluetooth broadcast by IR cameras and associated circuitry within Nintendo Wiimotes. Then, the signals are received by a PC and processed using pose extraction and stereo vision algorithms. The extracted motion and position parameters are used to manipulate a virtual object in the virtual reality toolbox of Matlab for 6-DOF motion tracking. We setup a stereo camera system with Wiimotes to increase the vision volume and accuracy of 3D coordinate estimation and present a 3D user input device implementation in C# with Matlab functions. The camera calibration toolbox is used for calibration of the stereo system and computation of the extrinsic and intrinsic camera parameters. We use the epipolar geometry toolbox for computation of epipolar constraints to estimate the location of the points which are not seen by both of the cameras simultaneously. Our preliminary results for stereo vision analysis indicate that the precision for pose estimation may reach to millimeter or sub-millimeter accuracy.