Systems and methods of hierarchical circuit partitioning are provided. More specifically, the invention utilizes a sliding window which is moved over portions of a hierarchical structure representing a programmable logic device. The window includes some but not all containers of the hierarchical structure so that logic cells may be partitioned within the window. After the logic cells are partitioned in the window, the window is moved to a different location of the hierarchical structure. By utilizing a sliding window, the invention is able to recursively partition logic cells into portions of the hierarchical structure which increases the overall efficiency of the partitioning.