Systems and methods of collecting blood cells, substantially free of undesired matter, use a first container (16), that forms a part of blood collection system (10), to initially collect a quantity of blood cells. A filtration system (14) is then attached to the first container. The filtration system (14) includes a second container (34), a first fluid path (36) that leads to the second container (34) through a filtration device (40), and a second fluid path (38) that leads to the second container (34) bypassing the filtration device (40). Blood cells are conveyed from the first container (16) through the first fluid path (36) and filtration device (40) and into the second container (34) to separate the undesired matter from blood cells. Blood cells, now substantially free of the undesired matter, are then conveyed from the second container (34) through the second fluid path (38), bypassing the filtration device (40), and back into the first container (16). The filtration system (14) is then detached from the blood collection system (10).