Apparatus, systems, and methods for forming a hole in biological material, such as tissue walls, adjacent vessels or adjacent regions of an organ such that access to opposing surfaces of the biological material can be achieved. In general overview the system may include ,an elongate member for positioning and deploying a flexible member in the heart. In one embodiment apparatus and methods are provided for aligning and fixing the position of the tip of a cutting member for cutting a hole in the septal wall of a heart. In another embodiment, subsequent to cutting a tissue wall an apparatus for obstructing holes in the septal wall is inserted to limit the flow of blood through a plurality of holes in a tissue wall.