A CT alignment system includes a central processing unit (CPU) that processes a plurality of CT images. The CPU determines a location of a main carina from the plurality of CT images and sets the main carina as a point of origin. An x-coordinate, a y-coordinate, and a z-coordinate is calculated for each pixel in each CT image among the plurality of CT images based on the point of origin. A 3D model is rendered from the plurality of CT images and the x-coordinate, the y-coordinate, and the z-coordinate for each pixel in each CT image is associated with a corresponding voxel in the 3D model. The x-coordinate, the y-coordinate, and the z-coordinate for each corresponding voxel in the 3D model is stored as voxel position data. A graphics processing unit (GPU) renders a three dimensional (3D) model based on the plurality of CT images and the voxel position data which is displayed on a display.