A head is disclosed for use with a manufacturing system. The head may have a housing configured to discharge a tubular structure reinforced with at least one continuous fiber and having a three-dimensional trajectory, and a cure enhancer operatively connected to the housing and configured to cure a liquid matrix in the tubular structure during discharge. The head may also have a nozzle configured to discharge a fill material into the tubular structure, and a wand extending from the housing to the nozzle.