Methods for the removal of an embolism protection device use aspiration during the drawing of the embolism protection device into the catheter. Generally, the embolism protection device comprises a three dimensional filtering matrix that provides improved filtering without blocking the flow through the patient's vessel. In some embodiments, the embolism protection device can be actuated between a deployed configuration and a removal configuration with a reduced area across the cross section of the vessel lumen. The embolism protection device in the removal configuration can be drawn within the aspiration catheter. The aspiration catheter can have a distal portion with an expanded compartment with an average diameter at least about 20 percent larger than the average diameter of the shaft of the catheter within about 10 centimeters of the expanded compartment. In a rapid exchange version, the rapid exchange segment can have a length of at least about 10 centimeters.