In this work we consider optimization problems for transport-reaction processes, when the cost function and/or equality constraints necessitate the consideration of phenomena that occur over widely disparate length scales. Initially, we develop multiscale process models that link continuum conservation laws with microscopic scale simulators. Subsequently, we combine nonlinear order reduction techniques for dissipative partial-differential equation systems with adaptive tabulation methods for microscopic simulators to reduce the computational requirements of the process description. The optimization problem is subsequently solved using standard search algorithms. The proposed method is applied to a representative thin film deposition process, where we compute optimal surface temperature profiles that simultaneously maximize deposition-rate uniformity (macroscale objective) and minimize surface roughness (microscale objective) across the film surface.