The upper voice coil motor magnet assembly (64a') of a disk drive (10') is magnetically aligned with the lower voice coil motor magnet assembly (64b') using an alignment fixture (126). The alignment fixture (126) engages the upper voice coil motor magnet assembly (64a') and lifts the same into a suspended position above the lower voice coil motor magnet assembly (64b'). In this suspended condition, the alignment fixture (126) allows the magnetic field to move the upper voice coil motor magnet assembly (64a') within the horizontal dimension to a magnetically aligned position with the lower voice coil motor magnet assembly (64b'). Thereafter, the alignment fixture (126) lowers the upper voice coil motor magnet assembly (64a') to a position where the same is again supported above the lower voice coil motor magnet assembly (64b').