A method for designing a patterning process for a three-dimensional (3D) memory includes defining a target 3D structure of the 3D memory, to be applied in a periodic structure of layers on a substrate. The target 3D structure is converted into a sequence of multiple steps, each step specifying a respective pattern to be removed and a respective number of the layers to be removed from the periodic structure under the respective pattern. The sequence of steps is sent to one or more manufacturing tools.