This work presents a novel extrinsic calibration estimation algorithm between a 3D Lidar and an IMU using an Extended Kalman Filter which exploits the motion based calibration constraint for state update. The steps include, data collection by moving the Lidar Inertial sensor suite randomly along all degrees of freedom, determination of the inter sensor rotation by using rotational component of the aforementioned motion based calibration constraint in a least squares optimization framework, and finally determination of inter sensor translation using the motion based calibration constraint in an Extended Kalman Filter (EKF) framework. We experimentally validate our method on data collected in our lab.