A method of controlling a medical tool includes determining an insertion path and pose for the tool based on a target and deploying first and second articulated arms of a computer-assisted medical device based on a size and shape of a tool guide. The arms include respective pluralities of moveable links actuated by at least one respective actuator and forming respective kinematic chains extending from a base. The method further includes receiving the tool guide for coupling with the arms using respective mounting arms of the tool guide such that the tool guide functions as a link in a closed kinematic loop formed by joining the kinematic chains, orienting a guide hole of the tool guide to align with the insertion path, positioning the guide hole a desired distance away from the target, receiving the tool in the guide hole, and advancing the tool along the insertion path.