A system for treating a patient having thrombus, comprising: an aspiration catheter (3000, 4000) having a distal end for placement into a blood vessel, a proximal end, and an aspiration lumen (3160, 4160) having an open distal end and extending between the distal end and the proximal end of the aspiration catheter (3000, 4000), the aspiration lumen (3160, 4160) configured to be coupled to a vacuum source; an elongate member (3102, 4102) having a distal end and a proximal end, the distal end having a straight distal portion such that the elongate member (3102, 4102) is configured to be inserted through the aspiration lumen (3160, 4160) of the aspiration catheter (3000, 4000), such that the distal end extends from the aspiration lumen (3160, 4160) into a thrombus within the blood vessel, wherein the elongate member (3102, 4102) includes a first portion configured to reside within the aspiration lumen (3160, 4160) and to facilitate the movement of partially or completely macerated thrombus through the aspiration lumen (3160, 4160) while the elongate member (3102, 4102) is moved in relation to the aspiration catheter (3000, 4000); a manipulation device (4231, 5231) comprising: a housing (4232, 5232) configured to be supported by the hand of a user, the housing (4232, 5232) having a distal end (4236, 5236) and a proximal end (4234, 5234); a drive system disposed within the housing (4232, 5232), and configured to rotate a rotation member (4207, 5207); an engagement member coupled to the rotation member (4207, 5207), and configured to be removably coupled to the elongate member (3102, 4102) to transfer rotational movement of the rotation member (4207, 5207) to rotational movement of the elongate member (3102, 4102); and an activation member (4214, 5214) carried by the housing (4232, 5232) such that it can be operated by at least a portion of the hand of the user when the housing (4232, 5232) is supported by the hand of the user; and wherein the drive system is configured to apply motive force to the engagement member to thereby move the elongate member (3102, 4102), wherein the motive force comprises a combination of motive force components comprising an alternating clockwise motion and counter-clockwise motion. an aspiration catheter (3000, 4000) having a distal end for placement into a blood vessel, a proximal end, and an aspiration lumen (3160, 4160) having an open distal end and extending between the distal end and the proximal end of the aspiration catheter (3000, 4000), the aspiration lumen (3160, 4160) configured to be coupled to a vacuum source; an elongate member (3102, 4102) having a distal end and a proximal end, the distal end having a straight distal portion such that the elongate member (3102, 4102) is configured to be inserted through the aspiration lumen (3160, 4160) of the aspiration catheter (3000, 4000), such that the distal end extends from the aspiration lumen (3160, 4160) into a thrombus within the blood vessel, wherein the elongate member (3102, 4102) includes a first portion configured to reside within the aspiration lumen (3160, 4160) and to facilitate the movement of partially or completely macerated thrombus through the aspiration lumen (3160, 4160) while the elongate member (3102, 4102) is moved in relation to the aspiration catheter (3000, 4000); a manipulation device (4231, 5231) comprising: a housing (4232, 5232) configured to be supported by the hand of a user, the housing (4232, 5232) having a distal end (4236, 5236) and a proximal end (4234, 5234); a drive system disposed within the housing (4232, 5232), and configured to rotate a rotation member (4207, 5207); an engagement member coupled to the rotation member (4207, 5207), and configured to be removably coupled to the elongate member (3102, 4102) to transfer rotational movement of the rotation member (4207, 5207) to rotational movement of the elongate member (3102, 4102); and an activation member (4214, 5214) carried by the housing (4232, 5232) such that it can be operated by at least a portion of the hand of the user when the housing (4232, 5232) is supported by the hand of the user; and wherein the drive system is configured to apply motive force to the engagement member to thereby move the elongate member (3102, 4102), wherein the motive force comprises a combination of motive force components comprising an alternating clockwise motion and counter-clockwise motion. a housing (4232, 5232) configured to be supported by the hand of a user, the housing (4232, 5232) having a distal end (4236, 5236) and a proximal end (4234, 5234); a drive system disposed within the housing (4232, 5232), and configured to rotate a rotation member (4207, 5207); an engagement member coupled to the rotation member (4207, 5207), and configured to be removably coupled to the elongate member (3102, 4102) to transfer rotational movement of the rotation member (4207, 5207) to rotational movement of the elongate member (3102, 4102); and an activation member (4214, 5214) carried by the housing (4232, 5232) such that it can be operated by at least a portion of the hand of the user when the housing (4232, 5232) is supported by the hand of the user; and wherein the drive system is configured to apply motive force to the engagement member to thereby move the elongate member (3102, 4102), wherein the motive force comprises a combination of motive force components comprising an alternating clockwise motion and counter-clockwise motion.