The present invention provides a method for exchanging catheters while containing emboli within a blood vessel such as a saphenous vein graft, coronary artery, carotid artery, or other similar vessels. A guidewire is inserted through the vasculature of a patient until it reaches a desired treatment site. A therapy catheter is then inserted over the guidewire until the distal end of the therapy catheter reaches the treatment site. The guidewire has a distally mounted balloon which is inflated to occlude the blood vessel. Then, the therapy catheter provides means for treating the vessel at the treatment site. After treatment, the therapy catheter is removed from the guidewire and exchanged with an aspiration catheter which rides over the guidewire until the distal end of the aspiration catheter reaches the treatment site. The aspiration catheter applies negative pressure to remove any emboli formed by the treatment procedure.