A CT alignment system comprising: a central processing unit that processes a plurality of CT image sets, the CPU processes each CT image set by performing the steps including: determining a location of a main carina, a right lobe carina, and a left lobe carina from a plurality of CT images (120 1, 120 2,... 120 n) in the CT image set; setting a reference plane based on the location of the main carina, the right lobe carina, and the left lobe carina; setting the main carina as a point of origin; calculating an x-coordinate, a y-coordinate, and a z-coordinate for each pixel in each CT image among the plurality of CT images based on the point of origin and the reference plane in an XYZ coordinate system; and rendering a 3D model from the plurality of CT images; associating the x-coordinate, the y-coordinate, and the z-coordinate for each pixel in each CT image with a corresponding voxel in the 3D model; and storing the x-coordinate, the y-coordinate, and the z-coordinate for each corresponding pixel in the 3D model as voxel position data; a graphics processing unit that processes the 3D model for each of the CT image sets in the plurality of CT image sets based on the voxel position data; and a display that displays a first 3D model for a first processed CT image set and a second 3D model for a second processed CT image set; wherein the main carina, the right lobe carina, and the left lobe carina form an XZ plane in the XYZ co-ordinate system; and wherein the z-coordinate for each pixel is equal to Z D ∗ cos α, where Z D is a distance along a line perpendicular to an XY plane between a CT image that includes the point of origin and a CT image that includes the pixel, and α is an angle at the point of origin between a z-axis and the line perpendicular to the XY plane. a central processing unit that processes a plurality of CT image sets, the CPU processes each CT image set by performing the steps including: determining a location of a main carina, a right lobe carina, and a left lobe carina from a plurality of CT images (120 1, 120 2,... 120 n) in the CT image set; setting a reference plane based on the location of the main carina, the right lobe carina, and the left lobe carina; setting the main carina as a point of origin; calculating an x-coordinate, a y-coordinate, and a z-coordinate for each pixel in each CT image among the plurality of CT images based on the point of origin and the reference plane in an XYZ coordinate system; and rendering a 3D model from the plurality of CT images; associating the x-coordinate, the y-coordinate, and the z-coordinate for each pixel in each CT image with a corresponding voxel in the 3D model; and storing the x-coordinate, the y-coordinate, and the z-coordinate for each corresponding pixel in the 3D model as voxel position data; determining a location of a main carina, a right lobe carina, and a left lobe carina from a plurality of CT images (120 1, 120 2,... 120 n) in the CT image set; setting a reference plane based on the location of the main carina, the right lobe carina, and the left lobe carina; setting the main carina as a point of origin; calculating an x-coordinate, a y-coordinate, and a z-coordinate for each pixel in each CT image among the plurality of CT images based on the point of origin and the reference plane in an XYZ coordinate system; and rendering a 3D model from the plurality of CT images; associating the x-coordinate, the y-coordinate, and the z-coordinate for each pixel in each CT image with a corresponding voxel in the 3D model; and storing the x-coordinate, the y-coordinate, and the z-coordinate for each corresponding pixel in the 3D model as voxel position data; a graphics processing unit that processes the 3D model for each of the CT image sets in the plurality of CT image sets based on the voxel position data; and a display that displays a first 3D model for a first processed CT image set and a second 3D model for a second processed CT image set; wherein the main carina, the right lobe carina, and the left lobe carina form an XZ plane in the XYZ co-ordinate system; and wherein the z-coordinate for each pixel is equal to Z D ∗ cos α, where Z D is a distance along a line perpendicular to an XY plane between a CT image that includes the point of origin and a CT image that includes the pixel, and α is an angle at the point of origin between a z-axis and the line perpendicular to the XY plane.