A fuzzy logic Run-by-Run(RbR) controller and an in -line wafer characteristics prediction scheme for the rapid thermal processing system have been developed for the study of process repeatability. The fuzzy logic RbR controller provides a framework for controlling a process which is subject to disturbances such as shifts and drifts as a normal part of its operation. The fuzzy logic RbR controller combines the advantages of both fuzzy logic and feedback control. It has two components : fuzzy logic diagnostic system and model modification system. At first, a neural network model is constructed with the I/O data collected during the designed experiments. The wafer state after each run is assessed by the fuzzy logic diagnostic system with featuring step. The model modification system updates the existing neural network process model in case of process shift or drift, and then select a new recipe based on the updated model using genetic algorithm. After this procedure, wafer characteristics are predicted from the in-line wafer characteristics prediction model with principal component analysis. The fuzzy logic RbR controller has been applied to the control of Titanium SALICIDE process. After completing all of the above, it follows that: 1) the fuzzy logic RbR controller can compensate the process draft, and 2) the in-line wafer characteristics prediction scheme can reduce the measurement cost and time.