A system for depositing a composite filler material into a channel of a composite structure includes an end-effector configured to extrude a bead of the filler material into the channel. The filler material can comprise a first group of relatively long fibers, a second group of relatively short fibers and a resin. A drive system is configured to move the end-effector relative to the channel, and a position sensor is configured to detect the position of the bead relative to the channel. A controller is configured to operate the drive system in response to the detected position and to operate the end-effector to heat and compress the filler material so as to orient the longer fibers in a substantially longitudinal direction relative to the channel and the shorter fibers in substantially random directions relative to the channel when the bead is extruded into the channel.