Certain aspects relate to systems and techniques for compensating for compression in elongated shafts of medical instruments. Medical instruments can include elongated shafts that may experience compression when articulated. The medical instruments can be attached to instrument positioning devices that are configured to move the medical instruments to compensate for this compression. For example, an instrument positioning device can advance a medical instrument to compensate for compression in an elongated shaft of the medical instrument. In some instances, the amount of compression is determined using a compression compensation parameter. The compression compensation parameter can be determined during a calibration process of the medical instrument.