Techniques are disclosed for optimizing the pattern density in the circuit layout design of a circuit layer. A layer in circuit design is analyzed to define empty regions that can be filled with fill polygons (referred to hereafter as “fill” regions). Next, a pattern of fill polygons is generated. After the fill polygons have been defined, the layout design for the layer is divided into separate areas or “windows,” and a target density for each window is determined. Once this target density for the window has been determined, the fill polygons required to most closely approach this target density are generated and added to the circuit layout design. This process may be repeated with progressively different (e.g., smaller) fill polygons, until each window meets or exceeds both the specified minimum density and complies with the specified maximum density gradient. Additionally, some implementations may allow a user to simultaneously optimize the density of multiple layers of a circuit by adding fill polygons to multiple layers of a circuit design simultaneously. Representations of sections of a multilayer fill structure will then be added to corresponding layers the circuit design until a specified target density is met.