A modular semiconductor substrate cleaning system is provided that processes vertically oriented semiconductor substrates. The system features a plurality of cleaning modules that may include a megasonic tank-type cleaner followed by a scrubber. An input module may receive a horizontally oriented substrate and rotate the substrate to a vertical orientation, and an output module may receive a vertically oriented substrate and rotate the substrate to a horizontal orientation. Each of the modules (input, cleaning and output) has a substrate support and may be positioned such that the substrate supports of adjacent modules are equally spaced. The modules are coupled by an overhead transfer mechanism having a plurality of substrate handlers spaced the same distance (X) as the substrate supports of the modules therebelow. The transfer mechanism indexes forward and backward the distance X to simultaneously transport semiconductor substrates through the cleaning system, lifting and lowering substrates from the desired modules wafer rotation/orientation sensors, an input module cart for transporting wafers between a substrate handler of a previous tool (such as a semiconductor substrate polisher) and a substrate handler of the cleaning system are also included.