A thrombectomy catheter deployment system which greatly simplifies setup procedures and operation of a thrombectomy catheter includes a stand alone drive unit and a disposable pump/catheter assembly which is manually placed into a carriage assembly in the drive unit. The pump/catheter assembly has a plurality of preconnected components including tubular structure and a thrombectomy catheter connected thereto and is transported into or out of the interior of the drive unit for automatic high pressure pump piston head engagement or disengagement with a reciprocating linear actuator and for automatic engagement or disengagement of an effluent waste tube with a roller pump. A barcode reader senses specific operational data pertaining to an individual pump and provides an interface for operation of the reciprocating linear actuator. A bubble trap incorporated for effective debubbling of saline solution is closely coupled to an insert molded pump having an improved valve arrangement. A spiked bag with large tubing is incorporated for bubble-free transfer of saline.