Apparatus and methods for treating in-stent restenosis are described for removing stenotic material from within previously stented regions of a patient's vasculature. The apparatus includes a catheter system having a stenotic material removal mechanism mounted on a distal portion of an elongated inner catheter. A sensing means, such as one or more sensing electrodes, are positioned on an outer surface of the apparatus. In addition, the apparatus optionally includes control means for diametrically expanding the stenotic material removal mechanism for effective recanalization of the stent. A coaxial outer catheter is provided for aspirating stenotic material which is removed from within the stent. In addition, embolic filter apparatus are described for collecting the stenotic material removed from within the stent. The methods comprise operating the stenotic material removal mechanism within a body vessel, typically a coronary artery or other artery, which has become restenosed or otherwise occluded following the initial stent placement, and sensing the proximity or contact between the stenotic material removal mechanism and the stent within the arterial wall so that the stenosis can be effectively recanalized without damaging the stent. The sensing means may be used to indicate an unsafe condition that might lead to stent damage, in response to which, the stenotic material removal mechanism may be manually or automatically deactivated. Alternatively or additionally, the sensing means may be used to indicate an appropriate endpoint for the stenotic material removal process.