Certain embodiments involve visually augmenting images of three-dimensional containers with virtual elements that fill one or more empty regions of the three-dimensional containers. For instance, a computing system receives a first image that depicts a storage container and identify sub-containers within the storage container. The computing system selects, from a virtual object library, a plurality of virtual objects that are semantically related to the sub-container. The computing system determines an arrangement of the virtual objects within the sub-container based on semantics associated with the sub-container and the plurality of virtual objects. The computing system generates a second image that depicts the arrangement of the plurality of virtual objects within the storage container and sub-containers. The computing system generates, for display, the second image depicting the storage container and the arrangement of the virtual objects.