LiDAR scanning has become a prevalent technique for digitalizing large-scale outdoor scenes. However, the raw LiDAR data often contain imperfections, e.g., missing large regions, anisotropy of sampling density, and contamination of noise and outliers, which are the major obstacles that hinder its more ambitious and higher level applications in digital city modeling. Observing that 3D urban scenes can be locally described with several low dimensional subspaces, we propose to locally classify the neighborhoods of the scans to model the substructures of the scenes. The key enabler is the adaptive kernel-scale scoring, filtering and clustering of substructures, making it possible to recover the local structures at all points simultaneously, even in the presence of severe data imperfections. Integrating the local analyses leads to robust shape detection from raw LiDAR data. On this basis, we develop several urban scene applications and verify them on a number of LiDAR scans with various complexities and styles, which demonstrates the effectiveness and robustness of our methods.