The self-assembly of known good dies (KGDs) on substrates using the liquid capillary method is shown to be a promising technology to achieve three-dimensional (3D) heterogeneous system integration and packaging. Firstly, the effects of the edge structures of self-assembled substrates and chips on alignment accuracies were investigated. When hydrophobic sidewalls with 10-μm-height steps were applied to both chips and assembly sites formed on substrates, the alignment accuracy within 1.0 μm was realized. The alignment accuracies were within 2.0 μm using either substrates or chips having 10-μm-height step structures with hydrophobic sidewalls. Self-assembly of 12-ch vertical-cavity surface-emitting lasers (VCSELs) with a long rectangle shape on glass substrates were also demonstrated. Separation of assembly sites into twelve areas enhanced the resultant force acting on the VCSEL short edge. The enhanced resultant force provided the high alignment accuracies within 2.0 μm. After the self-assembly of the VCSEL and the subsequent thermal compression, the chips successfully exhibited no degradation of their current-voltage (I-V) characteristics and appropriate 850-nm light emission. We demonstrated self-assembly and microbump bonding using non-conductive film (NCF)-covered dies with Cu/Sn microbumps for high-throughput and high-yield multichip-to-wafer 3D integration. The self-assembly of the NCF-covered dies provided high alignment accuracy within 1.1 μm on average. After the self-assembly of NCF-coved dies and thermal compression, microbump chains composed of 7396 bump joints were successfully obtained, resulting in good electrical properties of 32 mΩ/joint without any bridge shorts and failures. The variations of microbump joint resistance were maintained within 5% of the initial value after thermal cycle testing of even 1000 cycles.