A wafer handling system with apparatus for transporting wafers between semiconductor fabrication tools. In one embodiment, the apparatus is a loadport bridge mechanism including an enclosure having first and second mounting ends, a docking port at each end configured and dimensioned to interface with a loadport of a semiconductor tool, and at least one wafer transport robot operable to transport a wafer between the docking ports. The wafer transport robot hands off or receives a wafer to/from a tool robot at the loadports of a first and second tool. The bridge mechanism allows one or more wafers to be transferred between loadports of different tools on an individual basis without reliance on the FAB's automated material handling system (AMHS) for bulk wafer transport inside a wafer carrier such as a FOUP or others.