A manual clot aspiration and filtration system enables a method of removing a clot without general anesthesia and the expense of an operating room. An aspiration and filtration system for bodily fluid utilizes a syringe coupled with a filter unit to draw bodily fluid through the filter unit to collect debris on the filter. A flow valve may then be turned and the plunger depressed to force the filtered fluid back into the body. The filter may be configured to capture particles such as blood clots and plaque. The filter unit has a cover that can be removed for inspection and/or removal of the collected debris. When the cover is replaced, trapped air may be removed by turning the flow-valve to a purge direction and pressing the plunger into the syringe to force fluid back toward the filter unit to purge the trapped air through the purge valve.