A marking catheter made out of a flexible material and having a closed distal end and an open proximal end is provided. The marking catheter is sized and shaped to fit over the probe of a frameless stereotaxy system. One or more marking catheters may be positioned using the frameless stereotaxy system to define accurately an area identified in pre-operative imaging. For example, a plurality of marking catheters may be used to define physically the margins of a brain lesion. The brain lesion may then be removed to expose the positioned catheters, thereby assuring complete and effective lesion removal. The flexible catheters will move with any brain-shift occurring during lesion removal, thereby to maintain an accurate indication of the lesion margin.