A mechanism is provided for resolving patterning conflicts. The mechanism performs decomposition with stitches at all candidate locations to find the solution with the minimum number of conflicts. The mechanism then defines interactions between a layout of a first mask and a layout of a second mask through design rules, as well as interactions of mask1/mask2 with top and bottom layers (i.e., contacts, vial, etc.). The mechanism then gives the decomposed layout and design rule definition to any existing design rule fixing or layout compaction tool to solve native conflicts. The modified design rules are that same-layer spacing equals spacing of single patterning, different-layer spacing equals spacing of final layout, and layer overlap equals minimum overlap length.