Medical devices to treat stenosis, inhibiting restenosis, plaque removal, crossing totally occluded arteries or veins, treatment of vulnerable plaque, as well as removal of blood clots from the patient body arc disclosed. Such devices maybe used alone or in combination with therapeutic drugs. In some embodiments, flow protection devices are used for homogeneous drug delivery and removal from the patient to minimize the systemic effect. In some other embodiments, ablated tissue or blood clots are removed from the body after the procedure.