A shape-based geometric database uses R-trees to compactly and efficiently represent design objects. Such R-trees may be populated in an efficient and balanced manner to improve the efficient use of such R-trees in various stages of circuit design, for example. For example, tiles are assigned to bins depending at least partially on orientation of the tiles and on proximity of the tiles to reference tracks having similar orientations. Bin R-trees may be defined, along with direction and layer R-trees using a level sequential process from lower levels to higher levels until a root node is defined in each case.