A facility for cleaning substrates such as semiconductor wafers includes a loading/unloading part, an aligning part where wafers are repositioned from a horizontal state to a vertical state, a cleaning part performing etchant-treating, rinsing, and drying processes for wafers and having a plurality of process chamber stacked, and an interface part where a transfer bath is disposed to transfer wafers between the process chambers. When the wafers are transferred between the process chamber, the transfer bath is filled with deionized water (DI water) to prevent their exposure to the air. Wafers drawn out of the loading/unlading part are repositioned from a horizontal state to a vertical state and are transferred to a first process chamber being one of the process chambers to be subjected to a part of processes. After the wafers are transferred to a second process chamber being the other one of the process chambers to be subjected to the other processes, they are repositioned from a vertical state to a horizontal state. That is, the wafers are transferred along a loop shape to be processed.