Validation of the geometric data such as 3D city model is quite crucial for simulation tasks, since the simulation process strongly correlates to the quality of geometric data being meshed. Validation methodology and healing of the 3D city models using different tools are presented. The most common inherited geometrical errors are checked and analyzed. Accordingly, an appropriate healing process to the case study is performed, which illustrates that the required closed solids and closed shells are obtained within the geometrical structures of the 3D city model being processed. Also, in this paper we compare some related open source and commercial software tools for the validation and healing process. It is noticed that they differ from each other in performing the required healing process. Some of them are quite good in healing specific errors, whereas not successful in healing the rest of errors. The goal of the paper is to obtain more understanding of the geometric validation and healing capabilities of various software tools, and the qualities of generated meshes, to lead to more effective and reliable simulations in the field of urban wind flow simulation.