Mask optimization for layer based on comparison of components in layer to components in other layers

A non-transitory machine-readable medium storing a program which when executed by at least one processing unit optimizes a mask layout for producing masks for manufacturing an integrated circuit (IC) by defining multiple layers of components on a substrate, the program comprising sets of instructions for:

• generating, based on a first mask layout for the first layer, a simulated wafer image comprising representations of IC components that are predicted to be manufactured for a first layer of the IC;
• and
• comparing the simulated wafer image to a target wafer image comprising intended manufactured representations of the IC components for the first layer by quantifying differences between the predicted manufactured representations and corresponding intended manufactured representations of IC components, wherein the set of instructions for quantifying differences comprises a set of instructions for weighting the differences between the predicted manufactured representations and corresponding intended manufactured representations of IC components that interact with components in at least one additional layer of the IC more heavily than the differences between the predicted manufactured representations and corresponding intended manufactured representations of IC components that do not interact with components in any other layer of the IC;
• and
• based on the comparison, modifying the first mask layout to generate a modified second mask layout for the first layer.