Various implementations disclosed herein include devices, systems, and methods that uses object relationships represented in the scene graph to adjust the position of objects. For example, an example process may include obtaining a three-dimensional (3D) representation of a physical environment that was generated based on sensor data obtained during a scanning process, detecting positions of a set of objects in the physical environment based on the 3D representation, generating a scene graph for the 3D representation of the physical environment based on the detected positions of the set of objects, wherein the scene graph represents the set of objects and relationships between the objects, and determining a refined 3D representation of the physical environment by refining the position of at least one object in the set of objects based on the scene graph and an alignment rule associated with a relationship in the scene graph.