A method of operating an inkjet printer including an inkjet printhead having an ink inlet, the inkjet printhead mounted on a motor-driven carriage having an encoder sensor, the method including sending a signal from the encoder sensor to a controller to indicate a position of the motor-driven carriage; determining a velocity of the motor-driven carriage; implementing a first motion control mode during a period when the inkjet printhead is printing, wherein the first motion control mode includes a first signal for damping vibrations in order to provide a substantially constant velocity of the carriage; selectively implementing a second motion control mode when the inkjet printhead is not printing, wherein the second motion control mode includes a second signal for enhancing vibrations of the carriage in order to dislodge air bubbles in the printhead; and removing air corresponding to the air bubbles from the printhead.