In contrast to the single-light detection and ranging (LiDAR) system, multi-LiDAR sensors may improve the environmental perception for autonomous vehicles. However, an elaborated guideline of multi-LiDAR data processing is absent in the existing literature. This paper presents a systematic solution for multi-LiDAR data processing, which orderly includes calibration, filtering, clustering, and classification. As the accuracy of obstacle detection is fundamentally determined by noise filtering and object clustering, this paper proposes a novel filtering algorithm and an improved clustering method within the multi-LiDAR framework. To be specific, the applied filtering approach is based on occupancy rates (ORs) of sampling points. Besides, ORs are derived from the sparse “feature seeds” in each searching space. For clustering, the density-based spatial clustering of applications with noise (DBSCAN) is improved with an adaptive searching (AS) algorithm for higher detection accuracy. Besides, more robust and accurate obstacle detection can be achieved by combining AS-DBSCAN with the proposed OR-based filtering. An indoor perception test and an on-road test were conducted on a fully instrumented autonomous hybrid electric vehicle. Experimental results have verified the effectiveness of the proposed algorithms, which facilitate a reliable and applicable solution for obstacle detection.