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I'm trying to use a Shape Layer as a mask, but for some reason it is cutting random pieces out of the layer it is masking. The red shape is the mask, but why is there a random chunk out of the middle of my E? How do I fix this? There is no other shape layer or mask.
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Well, the internal shapoe clearly is a downscaled and squeezed version of the big shape, so it must come from somewhere. Without any info on how it looks in the timeline with properties revealed nobody can tell you much, though. This could be anything from messed up shape layer groups to using an effect liek Set Matte redundantly or incorrectly. Impossible to know.
Mylenium
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Not sure exactly what to show for troubleshooting because I'm new to After Effects, but here is some more detail. I am using Set Matte and Shape Layer 1 is the only shape layer in the composition at the moment.
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It looks like your shape layer might have a thick stroke instead of a mask.
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The stroke is set to 0px.
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Precompose your shape layer and use the 'move all attributes' option. Then select that precomp in the set matte effect.