An apparatus for depositing materials onto a micro-device workpiece includes a gas source system configured to provide a first precursor, a second precursor, and a purge gas. The apparatus can also include a valve assembly coupled to the gas source system. The valve assembly is configured to control a flow of the first precursor, a flow the second precursor, and a flow of the purge gas. Another component of the apparatus is a reaction chamber including an inlet coupled to the valve assembly, a workpiece holder in the reaction chamber, and an outlet downstream from the workpiece holder. The apparatus also includes a monitoring system and a controller. The monitoring system comprises a radiation source that directs a selected radiation through the reaction chamber and a detector that senses a parameter of the radiation directed through the reaction chamber. The controller is operatively coupled to the monitoring system and the valve assembly. The controller contains computer operable instructions to terminate the flow of the first precursor, the flow of the second precursor and/or the flow of the purge gas based on the parameter sensed by the monitoring system in real-time during a deposition cycle of a workpiece.