Methods and apparatus for removing emboli during an endarterectomy procedure are provided. The present invention provides a proximal catheter disposed proximal to a stenosis and a distal catheter disposed distal to the stenosis. Each catheter may selectively communicate with a venous return catheter via a manifold having a setting controlled by a physician. Blood flows into an aspiration lumen of the distal catheter and is reperfused into a remote vein via the venous return catheter. Additionally, emboli generated during the procedure are removed via an aspiration lumen of the proximal catheter, and filtered blood then is reperfused into the remote vein.