Hi Mocquin,
This is determined by the “Project Directory” options, in the “File“ menu bar and in the System Explorer
 

You can also access the opiotn in the zmx file, close to the top, with the line:
IWDP 1
1 means activated, 0 means deactivated.

Yes I know, so I deactivated the “project directory” option, but it still creates new empty folders when I open the zmx file

The ZMX file creating extra directories was saved as a lens project. The others were not. You can open it and convert back to a lens file from a lens project and it will not create the extra directories in the future. 

Thanks ​@Sean Turner but I’m not sure what you mean by “convert back to a lens file” ?

As of now, when I open the zmx file, it creates said folders, and the toolbar looks like this : 

and the file is not a “project directory” : 

Hi Mocquin,

If you open the file in a text editor, does it say
IWDP 1
or
IWDP 0
at the top ?
If 1, set it to 0 or remove the line (use a copy of the file if you want to be safe)

Line 5 in the file is : 

IWDP 0

Is it possible this comes from the fact that the file contains a blackbox row ?

​@mocquin 

I don’t know if it will help but you can also try what ​@Sandrine Auriol suggested here:

That is, with the ZOS-API:

TheSystem=TheApplication.PrimarySystem
TheSystem.TurnOffProjectDirectory()

I’m not sure if it does anything different than switching to IWDP 0.

Take care,

David

​@David.Nguyen  Yes I already tried that as well, with no effect...