A medical system including a flexible instrument such as a lung catheter or bronchoscope provides a control mode in which direct manual control of insertion can be used with computer-assisted control of instrument characteristics such as the orientation or rigidity of a portion of the instrument. To facilitate manual insertion control, a mechanism can provide low inertia and friction for movement along an insertion axis. One implementation employs a manual grip of the instrument for control of insertion pressure, a joystick or other input device for computer-assisted steering, and a foot pedal for control of stiffness or compliance in the instrument. Another implementation employs a joystick for computer-assisted steering and for control of stiffness or compliance in the instrument.