A filter retrieval system for retrieving a previously implanted medical filter, and methods of using the retrieval system, are disclosed. The filter retrieval system has a flexible shaft, a retrieval element, and a handle with an actuator. The flexible shaft may be catheter-based, and has a proximal and a distal end, and has an opening near its distal end. The handle is affixed to the shaft near the proximal end of the shaft, and the actuator is adapted to manipulate the retrieval element to grasp or hook or otherwise engage a portion of the filter, and then pull the filter in through the opening into a passage or lumen of the catheter shaft. The retrieval system is capable of retrieving a filter in into a proximal and distal space defined by the flexible shaft, though only one space at a time.