Researchers suffer from two problems in building a data processing pipeline for atmospheric scanning LiDAR. First, they must build an entire system that handles collecting signals, processing data, and visualizing results. Second, they should support fast data processing to expand and deploy their system. In this paper, we introduce MISE, a fast integrated system handling atmospheric scanning LiDAR data. MISE provides end-to-end processing, configuration options, and pre-defined signal processing methods. Also, the system uses an efficient chunking approach for fast processing with an array database. We demonstrate constructing and operating a fine-dust particles monitoring system (based on a real-world scenario) using MISE. This demonstration shows the usability and fast performance of MISE.