A semiconductor device fabrication apparatus is cleaned after a conductive layer is formed on a metal oxide layer of a substrate. The substrate is disposed on a heater in a process chamber of the apparatus, and the conductive layer is formed by introducing source gases into the chamber. Then the substrate is transferred out of the process chamber. At least one by-product of a reaction between the source gases and the metal oxide layer adheres to a surface inside the chamber, such as to a region or regions of the heater. Once the semiconductor substrate has been transferred outside the process chamber of the semiconductor fabrication apparatus, the by-product(s) is/are removed by evaporation. The by-product(s) can be evaporated using gas, such as one of the source gases, so that the process chamber can remain closed.