An ablation catheter system for capturing and removing necrotic tissue and thrombi generated during an ablative procedure is disclosed. The catheter typically includes an elongate member, a filtration assembly disposed within the distal region, and an ablation instrument at the distal end. Alternatively, the ablation instrument is carried on the distal end of an ablation catheter, which is disposed within a lumen of the catheter system. The catheter may further include an aspiration port and lumen. Methods of using the devices in preventing distal embolization during ablative procedures are disclosed.