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I am indexing a vector logo, because turning it into a shape and extruding it has not been working either. After a successful indexing, I return to the composition, and the logo bounding box shows a solid color around it. Blending modes do not seem to be nullifying the situation. This is frustrating, because the only other work around I can think of is to run it as an alpha in Z-brush, and repaint it. That, however runs risk of not looking exactly like the logo.
This may not be the best way to do it, but I have run the whole gambit of creating an AI file, and trying to convert it to a shape layer, yet, the bounding box is filled in, and I never even see my content, nor can it be manipulated, transformed, or used as a shape.
I have not been in the game for a while, but usually instruction videos and tutorials prove to be worthy and get the job done. This seems like a setting or a blending issue on the indexing project, but the shape layer project, (top screenshot), does not seem to be finding any path.
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I'm not clear what you are asking. Your gradient issue has been explained in your previous post - there is no way to retain AI gradients as editable shape layers. That and of course you designed your graphic in a way with all shading baked in so actual 3D geometry would not contribute much. The missing transparency is another issue, but I see no indication anywhere in your screenshots that there ever was actual transparency in the first place. So what exactly is the problem?
Mylenium
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I agree with Mylenium that this simply seems like a formatting issue with your Illustrator document and its transparency.
If you're going down the multiple-layers-to-create-extrusion road, as shown in your 3rd image (which is something I use all the time for quick 3D trickery) there shoud be no issue. Create a PNG or PSD of your logo at an appropriately high resolution, ensuring the background is empty and that the final image has transparency/alpha. It really should be that easy.
This looks like a perfect job for VCP's Element 3D plugin, BTW. It's great for fast real 3D of shiny metal logos etc.