The successful deployment of the Borexino solar neutrino detector required assorted physical and chemical operations to produce exceptional pure fluids and fill multiple detector zones. The composition and flow rates of high purity gases and liquids had to be precisely controlled to maintain liquid levels and pressures. The system was required to meet exceptional requirements for cleanliness and leak-tightness. A large scale modular system connecting fluid receiving, purification and fluid delivery processes was developed for Borexino. At the core is a flow control system that delivers scintillator components to plants for purification, and then fills the Borexino detector volumes with ultrahigh purity buffer or ultrahigh purity scintillator. The liquid handling system maintains precise control over the liquid levels and differential pressures between the different volumes of the detectors that are separated by flexible nylon vessels. The preparation, commissioning and operation of the system for filling the Borexino detector with scintillator is described.