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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