A system comprises a flexible instrument, an input device, an insertion drive system comprising a drive motor, and a control system configured to selectively switch between a computer assisted mode and a manual mode. In the computer assisted mode, the control system causes the drive motor to move the flexible instrument along an insertion axis in response to one or more signals received from the input device. In the manual mode, the control system causes the drive motor to become off or inactive to allow the flexible instrument to be manually moved along the insertion axis.