The quality of environmental perception is of great interest for localization tasks in autonomous systems. Maps, generated from the sensed information, are often used as additional spatial references in these applications. The quantification of the map uncertainties gives an insight into how reliable and complete the map is, avoiding the potential systematic deviation in pose estimation. Mapping 3D buildings in urban areas using Light detection and ranging (LiDAR) point clouds is a challenging task as it is often subject to uncertain error sources in the real world such as sensor noise and occlusions, which should be well represented in the 3D models for the downstream localization tasks. In this paper, we propose a method to model 3D building façades in complex urban scenes with uncertainty quantification, where the uncertainties of windows and façades are indicated in a probabilistic fashion. The potential locations of the missing objects (here: windows) are inferred by the available data and layout patterns with the Monte Carlo (MC) sampling approach. The proposed 3D building model and uncertainty measures are evaluated using the real-world LiDAR point clouds collected by Riegl Mobile Mapping System. The experimental results show that our uncertainty representation conveys the quality information of the estimated locations and shapes for the modelled map objects