This chapter is to identify the benefits and challenges of monolithic three-dimensional integrated circuits and to introduce physical design and tool solutions to address the challenges. The physical design and tool challenges of monolithic three-dimensional integrated circuits are addressed with the following three categories: design flow, power supply integrity, and application of monolithic three-dimensional integrated circuits. In design flow, an approach to implement monolithic three-dimensional integrated circuits is introduced. Power supply integrity issues of monolithic three-dimensional stacking technology are addressed. Lastly, deep neural network hardware using monolithic three-dimensional integrated circuits is presented as implementing low-power and high-performance deep neural network hardware is known to be difficult albeit they are widespread and powerful in recognition tasks.