Abstract: An end effector system for use with a robotic manipulator is disclosed for performing fastening operations with controlled torque while accommodating misalignment between fastener components. In some embodiments, the system includes a driving subsystem configured to engage a fastener component and apply rotational motion, and a holding subsystem configured to engage and stabilize a corresponding fastener component positioned on an opposite side of a fastening surface. At least one compliance mechanism can be operatively coupled to the driving subsystem or the holding subsystem and can provide controlled compliance along a selected axis while remaining substantially rigid along one or more other axes.