The present invention involves, in some embodiments, reusable pump drive systems, which are coupled to removable, and preferably disposable, pumping cartridges. The invention provides, in some embodiments, novel pumping cartridges for use in pumping systems. One such cartridge includes an integrated filter element therein for filtering fluids, for example fluids pumped to the body of a patient in a medical procedure. In some embodiments, the integrated filter is utilized as a blood clot removal filter and in other embodiments is used to remove particulates liquids infused to a patient. The filter element includes a filter with pores therein that are preferably sized to permit essentially unrestricted flow of individual human blood cells therethrough and to block or collect blood clots, cell clumps, particulates etc. with sizes substantially larger than the average size of a human blood cell.