Methods of harvesting cancellous bone and bone marrow include extracting loosened cancellous bone and bone marrow—including a liquid component thereof—to a collection container that has a first cup and a suction port to which a suction source is connected. After extraction, the suction source is disconnected and a lid of the collection container is removed and replaced with a lid having a plunger with a press head that is configured to filter the extracted liquid by depressing the plunger toward a bottom of the first cup. The filtered liquid is poured through a suction port into a second cup while depressing the plunger, thereby separating the liquid from a semi-solid mass of cancellous bone that remains. The bone is extracted through a cortical opening in the femur, tibia, or calcaneus, or from an intermedullary canal that is preferably formed by reaming of the tibia using an orthopedic reamer.