3D urban models created either interactively by human operators or automatically with reconstruction algorithms often contain geometric and semantic errors. Correcting them in an automated manner is an important scientific challenge. Prior work, which traditionally relies on local analysis and heuristic-based geometric operations on mesh data structures, is typically tailored-made for specific 3D formats and urban objects. We propose a more general method to process different types of urban models without tedious parameter tuning. The key idea lies on the construction of a kinetic data structure that decomposes the 3D space into polyhedra by extending the facets of the imperfect input model. Such a data structure allows us to rebuild all the relations between the facets in an efficient and robust manner. Once built, the cells of the polyhedral partition are regrouped by semantic classes to reconstruct the corrected output model. We demonstrate the robustness and efficiency of our algorithm on a variety of real-world defect-laden models and show its competitiveness with respect to traditional mesh repairing techniques from both Building Information Modeling (BIM) and Geographic Information Systems (GIS) data.