Disclosed is an improved approach for managing, tracking, and querying hierarchical data in layouts. According to some aspects, hierarchical grids are employed utilizing a scheme that organizes physical objects into a set of gradually refined grids that avoids the need to maintain duplicates while enhancing the desirable characteristics of existing schemes, including fast query times, fast data structure initialization and reduced memory footprint. Each grid-cell may be further partitioned into sub-containers to more efficiently provide space pruning during query operations. According to one approach, structures maintained to track existence of objects in a descendent hierarchy.