A method of designing a 3D Integrated Circuit including: partitioning at least one design into at least two levels, a first level and a second level, where the first level includes logic and the second level includes memory; and then obtaining a first placement of at least portion of the second level, where the first placement includes placement of a first memory array, where the Circuit includes a plurality of connections between the first level and the second level; and performing a second placement, where performing the second placement includes placing the first logic circuit based on the first placement of the first memory array, where the performing a second placement includes using a placer executed by a computer, where the placer is a part of a Computer Aided Design tool, and where the logic includes a first logic circuit configured to read data from the first memory array.