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Is there any way to extrude multiple layers with different depths?

I was trying to extrude a 2D to 3D using .dxf file and encounter the following problems:

  1. The extrusion is only possible for one single depth when I group it
  2. After the extrusion of multiple layers, it shifts and misaligned.

Hence, I created a reference square outside the clipboard and repeated in all layers. This made me possible to extrude different layers at different depths. The misalignment issue still persists.

How to fix the misalignment issue after separate the extrusion?

I have attached the AI file.

Adobe illustrator file][1]

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Illustrator is not a 3D "scene" tool. Its' "effect" is, at best, rudimentary and uses a localized XYZ axis, not global. Meaning each and every instance of the Effect uses it's own XYZ axis without any correlation to other instances of the effect on other objects. Illustrator's effect is designed to work on individual objects as a quick-apply type of thing for very basic 3D operations. It is simply not designed for settings or "scenes".

If you want to control extrusion/rotation on separate objects but have them all part of the same "scene" using global 3D reference points, you need an actual 3D application, not Illustrator.

Trying to create a 3D "scene" in Illustrator with separate objects can be a lesson in frustration.

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You have met one more thing where Illustrator works differently than CAD software.

The problem: 3D extrusion moves the extrusion result so that the bounding box center of the shown result is the same as the bounding box center of the original shape. See an example:

enter image description here

The 3D effect dialog allows no adjustment for this, some deeper knowledge is needed.

A workaround: If you expand the appearances of the extrusion results, you can realign them with the direct selection tool (=the white arrow)

enter image description here

After applying Object > Expand appearance to both shapes and deselecting all, the cyan shape was selected and the direct selection tool was taken to use. By dragging one of the anchors the whole shape moves. Only be sure that you have not clicked anywhere in the meantime.

If you have smart guides and snap to points ON, you can perfectly drag a corner to its right place and the rest of the shape follows. You must of course have corners which should match or separate marks.

In the next image the bigger cyan part has no common corners with the big green part. Small squares in the right are inserted (=grouped with the bigger shape of the same color) for alignment. They can be removed later.

enter image description here

NOTE: Use only parallel projections, adding perspective makes pieces which will not fit. That's because every piece will have its own camera placement and direction.

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