This paper describes the application of discrete event systems theory to the design of an automated laboratory system. Current automated laboratory systems typically consist of several interacting processes that must be carefully sequenced to avoid any possible process conflicts. Discrete Event Systems (DES) theory and Supervisory Control Theory (SCT) can be applied together as effective methods of modeling the system dynamics and designing supervisory controllers to precisely sequence the many processes that such systems might involve. Classical approaches to supervisory controller design tend to result in complex controller structures that are difficult to implement, maintain, and upgrade. In this paper, a new approach to designing supervisory controllers for automated laboratory systems is introduced. This new approach uses a modular controller structure that is easier to implement, maintain, and upgrade, and deals with "state explosion" issues in a novel and efficient way.