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Dear Miakatt,

For the sake of completeness, you could do the full inversion in Nazca and  I created a tutorial which reproduces roughly the Inverted MMI in the picture you posted.

Still, I would prefer to keep the waveguide and trench-overlay layers during the design process and do a post-design mask boolean operation in Klayout, i.e. do “Edit / Layer / Boolen operation” on the original waveguide and trench layer, or script that operation.