A control system for a harvester that harvests crop stalks each having a bottom portion and a top portion. The harvester includes a topper that cuts the stalks between the top and bottom portions and a base cutter that cuts the stalks near a ground surface. The control system includes a sensor that senses a first height between the top of the bottom portion and the ground surface, and senses a second height between the bottom of the bottom portion and the ground surface. The controller receives signals representing the sensed first and second heights from the sensor, determines average first and second heights for the stalks over a set time, sends a first signal to the topper to cause movement of the topper to the average first height, and sends a second signal to the base cutter to cause movement of the base cutter to the average second height.