A system for providing visual guidance for navigating inside a patient's chest, the system comprising: a cone beam computed tomography (CBCT) imaging device; a surgical tool (62,64, 90, 92, 93) having an electromagnetic position sensor; an electromagnetic navigation system for having an electromagnetic field generator for generating an EM field about the patient's chest and configured to detect the location of the position sensor within the EM field, and determine the position of a tool within the patient's chest based on the detected location of the EM sensor; and a computing device configured to generate a three-dimensional model of a luminal network, display an indication of the position of the tool on the 3D model, receive cone beam computed tomography (CBCT) image data of the patient's chest from the imaging device, detect the location of the tool within the patient's chest based on the CBCT image data, and update the indication of the position of the tool on the 3D model based on the detected location; characterized in that the computing device is further configured to provide guidance for positioning the CBCT imaging device based on the detected location of the EM sensor, the computing device being further configured to determine if the imaging device is within the EM field and, if so, to provide a notification that the EM field may be distorted based on the position of the CBCT imaging device and/or to compensate for distortion of the EM field or cause the field generator to compensate for the distortion based on the position of the CBCT imaging device. a cone beam computed tomography (CBCT) imaging device; a surgical tool (62,64, 90, 92, 93) having an electromagnetic position sensor; an electromagnetic navigation system for having an electromagnetic field generator for generating an EM field about the patient's chest and configured to detect the location of the position sensor within the EM field, and determine the position of a tool within the patient's chest based on the detected location of the EM sensor; and a computing device configured to generate a three-dimensional model of a luminal network, display an indication of the position of the tool on the 3D model, receive cone beam computed tomography (CBCT) image data of the patient's chest from the imaging device, detect the location of the tool within the patient's chest based on the CBCT image data, and update the indication of the position of the tool on the 3D model based on the detected location; generate a three-dimensional model of a luminal network, display an indication of the position of the tool on the 3D model, receive cone beam computed tomography (CBCT) image data of the patient's chest from the imaging device, detect the location of the tool within the patient's chest based on the CBCT image data, and update the indication of the position of the tool on the 3D model based on the detected location; characterized in that the computing device is further configured to provide guidance for positioning the CBCT imaging device based on the detected location of the EM sensor, the computing device being further configured to determine if the imaging device is within the EM field and, if so, to provide a notification that the EM field may be distorted based on the position of the CBCT imaging device and/or to compensate for distortion of the EM field or cause the field generator to compensate for the distortion based on the position of the CBCT imaging device.