Methods of packaging a medical device to orient at least a portion of the medical device and a medical device packaging assembly are provided. A method includes providing an elongate holder having a lumen extending through at least a portion of the holder and providing the medical device including an elongate shaft where the shaft includes a first cross-sectional area having a rotational orientation and a second cross-sectional area having a second rotational orientation. The method further includes aligning the first and second areas so that the first and second rotational orientations are aligned along a longitudinal region of the shaft and inserting at least a portion of the medical device into the lumen of the holder Radial rotation of the first area with respect to the second area is substantially prevented.