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I am trying to get the middle sphere to render as a part of the alpha for the image. In the image below where I have the test grid image at the moment it really should be transparent. How do I do that?

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If you are using cycles, all you have to do is use holdout sahder node. Give the object that you want to have the 0 alpha a new material like this.
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Then in the render tab of the properties window, under the Film section enable Transparent. You will have to save your render to a image format with a alpha channel, such as a .png.

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  • $\begingroup$ Woah I never knew of that shader before, thanks a million David! That worked just right! $\endgroup$ – pancreasboy Dec 22 '14 at 4:56
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These two nodes are all you need to add a object index pass to your render's alpha.
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First the ID Mask gets the right object. The the Mix node combines the render's alpha with the object index. The Object Index pass returns a black and white image, so that is just mixed, using itself as the factor with the original alpha. Last plug the new alpha in to the Alpha socket on the Composite node.

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