The purpose of the layout design is to find the most efficient arrangement of equipment, manpower in departments or units in order to maximize productivity in product production. Existing heuristic models do not consider the organizations need to locate units within certain departments, but in practice many organizations need to design a layout that limits the location of units in their respective departments. Particularly for organizations with an operational organizational structure, and often each of the units in each executive department should be located in their own office. The purpose of this article is that in an organization composed of several main departments and each department comprising several units, optimal placement is made in such a way that the limits of locating the units within the departments that are similar to the work process are met. Many layout design problems are not suited to solve mathematical problems because some of the facilities need to be put together. In this paper, constraints are added to design the facility layout in specific departments and a mathematical model is proposed for optimization. The benefits of introducing departmental constraints are: Compared to existing models, it provides more pragmatic logic for layout and facility design, and can help improve computational efficiency by reducing overlap constraints across facilities.