A medical navigation system (100, 800), comprising: a shape-sensing device which senses position and orientation along its length and generates corresponding SSD information (SSDI); a controller (122, 810) configured to: generate a three-dimensional volume based upon image information of a region of interest generated by an imager, determine a reference path to an object-of-interest situated within the ROI, the RP defining an on-road path through at least one natural pathway of an organ that moves due to cyclical motion of a patient and an adjacent off-road path through tissue of the organ leading to the OOI, and an exit point situated between the ONP and the ORP, query the SSD to obtain SSDI when the SSD is situated within the at least one natural pathway and is moving due to the cyclical motion, determine a shape and a pose of the SSD based upon the SSDI obtained when the SSD is situated within the at least one natural pathway and is moving due to the cyclical motion, determine deviation between the RP and the determined shape and pose of the SSD, and determine when to exit a wall of the natural pathway and begin the ORP, based upon the determined deviation. a shape-sensing device which senses position and orientation along its length and generates corresponding SSD information (SSDI); a controller (122, 810) configured to: generate a three-dimensional volume based upon image information of a region of interest generated by an imager, determine a reference path to an object-of-interest situated within the ROI, the RP defining an on-road path through at least one natural pathway of an organ that moves due to cyclical motion of a patient and an adjacent off-road path through tissue of the organ leading to the OOI, and an exit point situated between the ONP and the ORP, query the SSD to obtain SSDI when the SSD is situated within the at least one natural pathway and is moving due to the cyclical motion, determine a shape and a pose of the SSD based upon the SSDI obtained when the SSD is situated within the at least one natural pathway and is moving due to the cyclical motion, determine deviation between the RP and the determined shape and pose of the SSD, and determine when to exit a wall of the natural pathway and begin the ORP, based upon the determined deviation. generate a three-dimensional volume based upon image information of a region of interest generated by an imager, determine a reference path to an object-of-interest situated within the ROI, the RP defining an on-road path through at least one natural pathway of an organ that moves due to cyclical motion of a patient and an adjacent off-road path through tissue of the organ leading to the OOI, and an exit point situated between the ONP and the ORP, query the SSD to obtain SSDI when the SSD is situated within the at least one natural pathway and is moving due to the cyclical motion, determine a shape and a pose of the SSD based upon the SSDI obtained when the SSD is situated within the at least one natural pathway and is moving due to the cyclical motion, determine deviation between the RP and the determined shape and pose of the SSD, and determine when to exit a wall of the natural pathway and begin the ORP, based upon the determined deviation.