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OK, I know the question is kinda usual. My problem is I want some objects in a scene completely transparent/invisible (in most of the render passes) while I still can show it in either material or object index pass. I would avoid duplicate the scene because it's quite large and complicated and the less labor, the merrier.

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  • $\begingroup$ Fully transparent material does not give material index pass, but partially transparent does. Maybe it is a bug. $\endgroup$ – Jaroslav Jerryno Novotny Nov 18 '16 at 15:52
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In Cycles you can adjust the Alpha Threshold for the Render Layer to adjust how layers are affected by transparency. Setting the Alpha Threshold to 0.000 will result in all objects - even those that are completely transparent - affecting the Index passes (as well as the Z, Normal, UV, and Vector passes).

Alpha Threshold

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