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The association of a high-level semantics to the geometric components of 3D worlds for the net is gaining popularity, because it enables advanced uses of the 3D objects and it may improve their findability, extended to a network of annotated 3D worlds. Most of the proposals for annotating 3D worlds for the net are characterized by top-down approaches, where selected authors annotate 3D worlds in relation to predefined classes and relations. A different approach - introduced only in recent times for the 3D web but widely diffused in the hypertextual web - permits to users to annotate freely objects and spaces, originating bottom-up structures defined as folksonomies. This work introduces a web-based specification, a software architecture and a set of interfaces for annotating 3D worlds. The proposal is based on the X3D standard and enables both top-down and bottom-up annotation styles. The components of the software architecture - named ToBoA-3D - can be used in different scenarios, ranging from the complete management of a centralized set of annotated 3D worlds to the creation of a network of top-down annotated 3D worlds distributed on the net. Besides, the solution proposed can be applied to many X3D worlds already available on the net, without compromising the interaction possibilities implemented by the world designers. The architecture includes a search module that may use the annotations retrieved during the browsing phase for triggering the research of other objects and spaces that share the same labels but are part of other 3D worlds. The integration of navigation and searching - introduced in ToBoA-3D but unavailable for most of the 3D worlds for the net - represents an additional feature that may improve furthermore the findability of the resources. The paper defines also an enhanced model for defining the spatial limits of complex spaces, that is used as a basis for annotating these entities. The presentation of the user interfaces, applied to an example related to the architectural domain, concludes the work.