Methods and apparatus for maintaining sterility during transluminal procedures are described. The sterility is achieved by making use of a membrane in either the form, e.g., of a sheath, cap or umbrella to keep the instruments (endoscopes, overtubes, etc.) sterile while being advanced through lumens in the body and into the various cavities. Methods, such as vacuum acquisition, mechanical tissue anchoring, etc., of the underlying tissue followed by incision of the tissue with, e.g., a needle knife, can be utilized to gain access to the various cavities. It is expected that this procedure will provide the desired level of sterility for transluminal procedures.