Disclosed herein are devices, systems and methods for in-line, nanoscale metrology. One system comprises monolithic flexure mechanisms with integrated actuators that allow movement and positioning in two axes, with an extremely high degree of accuracy, of a structure comprising one or more scanning probes. This structure is suspended to prevent any destructive interference from a sample, which can be stationary or moving at a nonzero rate, and rigid or flexible in mechanical behavior. This system can be activated at startup and quickly actuate the structure to approach the surface of the sample. Once the system achieves the desired proximity between the one or more probes and the sample, the system maintains that position of the structure to a high degree of accuracy regardless of any disturbances. This array can be moved at varying speeds laterally to match the velocity of any continually moving substrates, thus enabling scanning of moving substrates.