The present teaching relates to method, system, medium, and implementations for estimating 3D coordinate of a 3D virtual model. Two pairs of feature points are obtained. Each of the pairs includes a respective 2D feature point on an organ observed in a 2D image, acquired during a medical procedure, and a respective corresponding 3D feature point from a 3D virtual model, constructed for the organ prior to the procedure based on a plurality of images of the organ. The depths of the first and the second 3D feature points are substantially the same. A first 3D coordinate of the first 3D feature point and a second 3D coordinate of the second 3D feature point are automatically determined based on the pairs of feature points so that a first distance between the determined first 3D coordinate and the determined second 3D coordinate equals to a second distance between a first actual 3D coordinate of the first 3D feature point and a second actual 3D coordinate of the second 3D feature point in the 3D virtual model.