A drilling system includes a single robotic drilling unit having a drill end effector positioned inside a barrel section configured as a composite sandwich structure having an inner face sheet. The robotic drilling unit is operable to drill a plurality of perforations into the inner face sheet using the drill end effector. The robotic drilling unit is configured to index a hole pattern of the perforations to one or more cell walls of a honeycomb core of the composite sandwich structure. The robotic drilling unit is configured to form the hole pattern in the inner face sheet such that the perforations are located at a spaced distance from the cell walls of the honeycomb core.