A computer-assisted medical system includes a manipulator arm and a controller. The controller includes a computer processor and is configured to determine a kinematic configuration, the kinematic configuration being prior to an installation of a replacement tool on the manipulator arm. The kinematic configuration is of the manipulator arm and a previous tool attached to the manipulator arm and with an end effector of the previous tool located at an insertion location. The controller is further configured to determine a reference geometry of the previous tool in the kinematic configuration, determine an insertion trajectory for the replacement tool based on the reference geometry, and facilitate an insertion of the replacement tool toward a target location of the insertion trajectory by controlling the replacement tool to move in accordance with the insertion trajectory.