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The occupied cells are specified in the file responsible for the object on the map.
There, each cell is a separate item with coordinates.
And this item can be assigned to be either an active or inactive cell.
Also, in the same file, you can define "empty" cells under the object if the model extends below the surface level. For example, this is how the cities of demons and dark elves are created, with gaps in the city.
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To make the same object smaller, you can export a reference object from the game, something that occupies exactly one cell (the dwarves have some kind of fiery sewer grate) and adjust the size in Max.
Or, you can add the model as an effect on top of the object and edit the size of the effect.