This invention discloses methods to reconfigure highly scalable and modular automated optical cross connect switch devices comprised of large numbers of densely packed fiber strands suspended within a common volume. In particular, methods enabling programmable interconnection of large numbers of optical fibers (100's-1000's) are provided, whereby a two-dimensional input array of fiber optic connections is mapped in an ordered and rule-based fashion into a one-dimensional array. A particular algorithmic implementation for a system reconfigured by a three-axis robotic gripper as well as lateral translation of each row in the input port array is disclosed.