A method for positioning an input device of a workstation for use by a seated user in controlling a robotic surgery system is disclosed. The input device is operable to generate input signals representing a position of a hand controller moveable within an input device workspace. The method involves determining a vertical position of the hand controller within the input device workspace for an input signal received from the input device while a seated user's hand is grasping the hand controller in an initialization position defined with respect to the user's body. The method also involves determining a user ergonomic height of the input device based on the vertical position of the hand controller at the initialization position, and causing a platform of the workstation on which the input device is mounted to move vertically with respect to a base of the workstation to position the input device at the ergonomic height.