A method for guiding an instrument associated with a medical device, such as an endoscope, is provided. The method is useful for positioning a flexible medical instrument extending from an instrument channel of an endoscope, such as for the treatment of tissue. The method is also useful for providing cooperative motion between first and second instruments extending from instrument channels within a patient's body lumen. In one embodiment, the step of guiding the instrument comprises bending the instrument as the instrument extends from the instrument channel.