A target substance, such as a thrombus, is removed from a patient's body via minimally invasive technique. A catheter is maneuvered and positioned near the target substance. The catheter may have a soft, atraumatic tip constructed from a metallic backbone covered by a polymer. Target substances are drawn into the catheter via an aspiration source. Near the catheter's distal end, a blade and opposing surface are housed within the catheter, and the blade moves relative to the opposing surface within the catheter lumen in order to fragment the target substance. The substances are fragmented within the catheter into discreet and relatively uniform particles. The aspiration source, which helps ensnare target substances, also serves to evacuate the substance fragments from the patient's body.