This study focuses on the optimal control of rapid thermal annealing (RTA) used in the formation of ultrashallow junctions needed in next-generation microelectronic devices. Comparison of different parameterizations of the optimal trajectories shows that linear profiles give the best combination of minimizing junction depth and sheet resistance. Worst-case robustness analysis of the optimal control trajectory motivates improvements in feedback control implementations for these processes. This is the first time that the effects of model uncertainties and control implementation inaccuracies are rigorously quantified for RTA. (C) 2003 Elsevier Ltd. All rights reserved.