One aspect of the invention is directed toward a method of forming a conductive layer on a microfeature workpiece. In one embodiment, the method comprises placing a microfeature workpiece in a vapor reaction chamber, depositing an electrically conductive material onto the microfeature workpiece in a vapor deposition process by flowing a gas into a plasma zone of the vapor deposition chamber and transmitting energy into the plasma zone via a transmitting window. The energy transmitted through the window and into the plasma zone produces plasma from the gas. The plasma produced from the gas forms a conductive layer on the workpiece and a residual film on the window. This embodiment of the method further includes changing the residual film on the window to have a reduced transmissivity to the energy.