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A 3d layer located in the center of the screen rotated on the Y axis to either 90 or -90 will not disapper even when opacity is at 0. Apparently the layer must be a -89 or anything besides +/-90 for zero opacity to kick in.
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Try selecting Layer/Hide Layer Controls. A layer has no thickness. It is not 1 pixel in Z; it is zero. When you rotate it 90º to the camera, the layer controls show up, but they will not preview or render. Even if the opacity is set to 100%, a layer 90º in X or Y to the camera will not render or show up in a preview. You could stack up 100 layers and have them all parallel to the nodal point of AE's lens and offset by 1 pixel, and you still would not get any of the layers to render. It's been that way for as long as I can remember.
Check out this comp. I used expressions to make each layer perpendicular to the active camera and offset each copy by one pixel in X., The custom view shows a nice 100-pixel thick stack of layers, but the active camera shows nothing when previewed because the layers have no thickness, only X and Y dimensions.
The expressions:
//Position
[value[0] + index, value[1], value[2]]
// orientation:
R = lookAt(position, thisComp.activeCamera.position);
[R[0], R[1] + 90, R[2]]
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I agree with Rick that it sounds like you're just seeing the controls.
But if that's not the case, post a screengrab of your project with the timeline, rotation and opacity settings vsisble.