An additive manufacturing system opens the valves in an extruder needed to form a swath and operates an actuator to move the extruder through a transition region with those valves open to establish an amount of extrusion material between a faceplate of the extruder and a portion of an object being formed that is adequate for formation of a swath. The length of the transition region is determined with reference to a viscosity of the material being extruded and a speed at which the extruder is moved to form the swath. The transition region can be perpendicular to a path of the extruder to form the swath or aligned with the path of the extruder to form the swath.