Archaeological recording is intended to preserve as much information as possible about the finds. However, once the pieces are removed from the site, there is information regarding the original positioning of these pieces that may be lost or not accurately recorded and can be relevant for further studies. This spatial arrangement can also be crucial for subsequent piece restoration or to understand certain aspects of ancient cultures. In this article, we describe a software prototype and a methodology to virtually reconstruct an archaeological site for posterity, once it has been excavated. The system is implemented with a client-server architecture. In the server, a spatial database stores and manages the three-dimensional (3D) models of the finds, as well as several 3D site ground surface models acquired at different times during the excavation process. On the client side, a graphical interface allows the user to manipulate the find models to re-create and virtually reconstruct the original spatial arrangement of the archaeological site. Topological relationships among the finds are stored in the database to provide further spatial analysis. The result is an integrated information system that goes beyond 3D visualization, making the site last for posterity after its excavation and allowing further spatial analysis.