High mobility electron gases confined at material interfaces have been a venue for major discoveries in condensed matter physics. Ultra-high vacuum (UHV) technologies played a key role in creating such high-quality interfaces. The advent of two-dimensional (2D) materials brought new opportunities to explore exotic physics in flat lands. UHV technologies may once again revolutionize research in low dimensions by facilitating the construction of ultra-clean interfaces with a wide variety of 2D materials. Here, we describe the design and operation of a UHV 2D material device fabrication system, in which the entire fabrication process is performed under pressure lower than 5 × 10-10 mbar. Specifically, the UHV system enables the exfoliation of atomically clean 2D materials. Subsequent in situ assembly of van der Waals heterostructures produces high-quality interfaces that are free of contamination. We demonstrate functionalities of this system through exemplary fabrication of various 2D materials and their heterostructures.