The present teaching relates to method and system for aligning a virtual anatomic model. The method generates a virtual model of an organ of a patient, wherein the virtual model includes at least three virtual markers. A number of virtual spheres equal to a the number of virtual markers are generated, wherein the virtual spheres are disposed on the virtual model of the organ of the patient and associated with the virtual markers. A first position of the virtual spheres and the virtual markers is recorded. The virtual spheres are placed to coincide with physical markers disposed on the patient and a second position of the virtual spheres is recorded. A transformation of the virtual spheres and the virtual markers based on the first and second positions is computed and the virtual model of the organ is aligned with the patient based on the computed transformation.