The CMS experiment at CERN's Large Hadron Collider will search for new physics at the TeV energy scale. Its trigger system is an essential component in the selection process of potentially interesting events. The Global Trigger is the final stage of the first-level selection process. It is implemented as a complex electronic system containing logic devices, which need to be programmed according to physics requirements. It has to reject or accept events for further processing based on coarse measurements of particle properties such as energies, momenta, and location. Algorithms similar to the ones used in the physics analysis are executed in parallel during the event selection process. A graphical setup program to define these algorithms and to subsequently configure the hardware has been developed. The design and implementation of the program, guided by the principal requirements of flexibility, quality assurance, platform-independence and extensibility, are described.