An apparatus for applying surgical fasteners to tissue is disclosed. The apparatus includes an actuator, an applicator section for applying the fasteners and a transversely flexible shaft connecting the applicator and the actuator. The actuator and applicator preferably each contain a hydraulic fluid chamber. The chambers communicate via a hydraulic line contained in the flexible shaft. Actuation of the instrument causes movement of a piston in the applicator fluid chamber, which causes application of the fasteners. A similar second hydraulic system is preferably provided for adjusting the axial position of an anvil used to clinch the fasteners. The two hydraulic control systems are operable wholly independently of each other, permitting precise control of the anvil pressure on the tissue.