HNY…
I have drawn this Arabic Jeem and want to get only the back shape without the green box, at the same time, I don’t want to lose the original drawing (points) of the back shape. yes, I need it only in the designing stage. because I want to play with this edge in bolder thickness, but, I will not need it in the final stage (exporting).
You can use the Mask feature, new in Glyphs 3. Select the box and check Mask 
:
If you don’t see the checkbox in the lower right, press Command-Shift-I.
The mask-path must be above the other path. If it is not, you can select the mask-path, copy it, delete it, and paste it again. (Not sure if this is the best way, but it works for me.)
Here is a demo file where you can see the effect from the screenshot above:
Test.glyphs (6.0 KB)
I did have look and there is a better way: Menu → “Filter” → “Shape Order”.
or, if you’re on glyphs 2, you can achieve the same without the mask tool, like shown in this screencast:
I’m trying to convert this font project to variable font, but it seems that the variable format conflicts with “Mask” feature , or something else, would you please advise,
The problem is that, after subtraction, the resulting path structure has to be compatible for a variable font export.
Very likely the mask covers one point more in one master, one less in another. The resulting paths are therefore incompatible.
ok, thank you for your advice, I have rearranged my paths/shapes, and I solved it, but still giving me this message :
& this was the issue: / solved.
the error in .notdef means you have a unsupported master setup.
