Packaging continues to be one of the most challenging steps in micro-nanofabrication, as many emerging techniques (e.g., soft lithography) are incompatible with the standard high-precision alignment and bonding equipment. In this paper, we present a simple-to-operate, easy-to-adapt packaging strategy, referred to as Capillary-driven Automatic Packaging (CAP), to achieve automatic packaging process, including the desired features of spontaneous alignment and bonding, wide applicability to various materials, potential scalability, and direct incorporation in the layout. Specifically, self-alignment and self-engagement of the CAP process induced by the interfacial capillary interactions between a liquid capillary bridge and the top and bottom substrates have been experimentally characterized and theoretically analyzed with scalable implications. High-precision alignment (of less than 10 µm) and outstanding bonding performance (up to 300 kPa) has been reliably obtained. In addition, a 3D microfluidic network, aligned and bonded by the CAP technique, has been devised to demonstrate the applicability of this facile yet robust packaging technique for emerging microfluidic and bioengineering applications.