To enhance its control efficiency, for a new class of discrete event systems, i. e. high throughput screening(HTS) systems, it is modeled within both event- and time- domain under the framework of dioid. For optimal control of many discrete event systems, desired input-output model behaviour is an objective commonly considered. However, according to practical control requirements of HTS systems, more often, desired state trajectories or desired output trajectories are considered. Therefore, dioid-based optimal control structures with different objectives are studied. State-feedback and output-feedback structures are discussed, respectively. Finally, some examples are given to illustrate the application of the aforementioned control structures. Simulation results show the effectiveness of the proposed optimal control.