Hi Anna, It sounds like you're talking about the 'Check registered models' step of the first stage in Customizer (Head Model Preparation). When you load the internal mean mesh into that window, it doesn't matter what the orientation is, the only thing that matters is that it matches your head mesh (which you also load into that window). So feel free to rotate around to confirm that the 2 surfaces are well aligned. As long as the 2 surfaces are well matched, any other surfaces in the same coordinate system should then integrate correctly in the subsequent stages.
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