This paper reports on a successful 3D integration (3DI) of multi-purpose signal processor (MSP) chips with memory chips using die-to-wafer (D2W) and wafer-to-wafer (W2W) bonding technologies. 3D integration enables compact systems of commercial-off-the-shelf (COTS) parts with high functionality using a wafer-level process for better thinning process uniformity and high yield throughput. The3D system is comprised of commercial Flash memory bare die and MSP bare die. The bare die are face-down aligned to a 150mm diameter silicon handle wafer with alignment marks polished silicon surface. Unique features on the commercial die are detected and used for die registration using a flip-chip bonder with vision automation. An adhesive film between the die and silicon handle wafer are used for temporary bonding. After the die-to-wafer population and bonding, the die substrates are thinned at the wafer-level to a target of 60 microns for the memory die and 25 microns for the MSP die, respectively. The thinned memory die set is permanently transferred onto a 150mm diameter silicon carrier wafer using a low temperature silicon covalent wafer bonding. Following bonding, an adhesive film release process is used to separate the memory die set from the temporary handle wafer. The thinned MSP die on a second handle wafer are then aligned to the thinned memory die set using a wafer-to-wafer alignment tool, and bonded with thin-film polyimide in a high-yield, low temperature wafer bonding process, followed by the release process to separate the MSP die set from the handle wafer. Finally, the MSP/memory stack are electrically connected using a via-last through-silicon-via (TSV) process. One of the key considerations for COTS 3DI is to meet the back-end-of-line (BEOL) thermal budgets of 350–400 Celsius. Plasma-assisted preparation facilitates the reduction in thermal budget for silicon covalent bonding and is performed at 150 Celsius, followed by a long-term annealing process at 175 Celsius. Stacking of thinned die relies on low temperature polyimide bonding that is performed at 200 Celsius. Fluorine and oxygen based plasma surface activation process and CTE-matched polyimide bonding play a critical role in enabling the low temperature bonding for this 3D MSP/memory integration. The thinning and bonding processing details that are presented in this paper are essential for COTS 3DI but can also be applied to several low-profile multi-chip module and packaging applications.