A method and system for laser based instrument registration. The system includes an operating table coupled with a robot holding an instrument, and CT scanner. The CT scanner has first and second laser markers. The method includes moving the robot to align the instrument in a first position wherein a tip of the instrument is disposed within a first laser plane created by the first laser marker. Then, the robot moves the instrument to a second position wherein the entire instrument is disposed within the first laser plane. Coordinate data of the robot in the second position is obtained. Image data of a first slice is obtained from the CT scanner. The registration data is calculated based on the coordinate data and the image data.