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I put a rep frigate in ZE in a land map I am making and strategically placed it ontop of a hangar so that it would cover up the giant open spot at the top. In ZE it appears directly ontop of the hangar but ingame it is about 12meters too high. I am not sure if anyone has had this problem before, but if you know how to fix it I would appreciate it.

Try either lowering it until it looks right ingame or doing a clean.

Look at it from different views in ZE. Fiowne had this problem with his geonosis map, and I dont think hes fixed it yet. It coult just be a simple ze error though.

Is it a custom object? If the object wasn't centered to 0, 0, 0 on export that might cause an issue. I'm not a modeler, so I dunno.

No it is not a custom object. This has me really stumped. Maybe I should try cleaning or something.

In ZE object placement editor on the side bar you will see something that says Ground to:
and below that you will see Terrain and Object boxes
Click on the Object box. Then select your object from the list the click on the Ground Object.
That should snap your selected object to the object below it. If you wanted to ground to terrain you would select the terain box first then Gound Object.

If it doesn't, as Teancum mentioned, have the model centered around 0,0,0 then grounding object won't necessarily work.

If you think it is 12 M to high you can also just subtract 12 from the height indicated in the Height box, once again in ZE just under where is says Properties.