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It seems backwards to me that the clipping mask layer is below the layer that you want masked. If I'm looking down through the layers, why wouldn't the clipping mask layer be on top of the layer I want masked? I am missing something fundamental about how to understand Photoshop (or other like programs).

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Because in the Layers palette, it is always true that you see the layer that lies on top, not the one on the bottom. This hard rule would be violated if the positions were inverted and confuse a lot of issues that way.

Think of it less like an actually cut-out mask and more like you apply, 'rub off', the top layer to the bottom layer. The top layer can only show there where the bottom layer is present, because you can't rub something off on nothing, can you?

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Here some points extracted from photoshopessentials.com

Clipping masks use the content and transparency of the layer below to control the visibility of the layer above.

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As you move the image, only the area that moves over the shape on the layer below it remains visible. And that's the basics of how clipping masks work.

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A clipping mask is not a window to see through, it would be the case of the mask above:

enter image description here

But a frame where to place an image, the mask below.

frame

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