A system for multi-scale closed-loop eye tracking to compensate for translation and rotation motion while imaging in vivo a surface area of an internal structure of an eye of a subject includes a narrow field imaging device optically coupled to an optical path to receive light reflected from the surface area of the structure of the eye. A wide field camera is optically coupled to the optical path by a beam splitter disposed in the optical path. A tracking mirror is disposed in the optical path between the beam splitter and the structure of the eye. A control process algorithm actively compensates substantially in real time for both translational and rotational movements of the eye. A system where a torsional correction device causes a rotating movement of a subjects head and a method for multi-scale closed-loop eye tracking are also described.