Flexible organic single crystals are evolving as new materials for optical waveguides that can be used for transfer of information in organic optoelectronic microcircuits. Integration in microelectronics of such crystalline waveguides requires downsizing and precise spatial control over their shape and size at the microscale, however that currently is not possible due to difficulties with manipulation of these small, brittle objects that are prone to cracking and disintegration. Here we demonstrate that atomic force microscopy (AFM) can be used to reshape, resize and relocate single‐crystal microwaveguides in order to attain spatial control over their light output. Using an AFM cantilever tip, mechanically compliant acicular microcrystals of three N‐benzylideneanilines were bent to an arbitrary angle, sliced out from a bundle into individual crystals, cut into shorter crystals of arbitrary length, and moved across and above a solid surface. When excited by using laser light, such bent microcrystals act as active optical microwaveguides that transduce their fluorescence, with the total intensity of transduced light being dependent on the optical path length. This micromanipulation of the crystal waveguides using AFM is non‐invasive, and after bending their emissive spectral output remains unaltered. The approach reported here effectively overcomes the difficulties that are commonly encountered with reshaping and positioning of small delicate objects (the “thick fingers” problem), and can be applied to mechanically reconfigure organic optical waveguides in order to attain spatial control over their output in two and three dimensions in optical microcircuits.