A method for assisting in the performance of a surgical procedure on a patient is disclosed. The method includes receiving an intra-operative CT scan image, generating a three-dimensional isotropic scaffold based on the intra-operative CT scan image, fusing one or more images with the three-dimensional isotropic scaffold to form a three-dimensional model of a portion of the body of the patient, receiving information regarding the surgical procedure, determining obstacles in the path of the surgical procedure, and determining possible trajectories for the surgical procedure. The received information includes information regarding a surgical target to be operated upon, a region of access on the skin of the patient, and a surgical instrument to be used during the surgical procedure.