How do I apply the mirror modifier properly, I am using the Fuselage as the mirror point, but as soon as I hit apply the flaps get all wonky. what do I need to do to make it work fine?
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What do you use for animation? Armature, shape keys, or setting keyframes. Because it really depends on which one you use.
Check out the ORDER of modifiers. If your Armature modifier is below your mirror modifier, switch the order.
I doubt you use shape keys because you cannot use mirror modifiers with shape keys. But just in case, check this out. Briefly explained, you can use "mirror shapekeys" at the black triangle below the add-shapekey-button.
I believe you have nothing set as a mirror object (of mirror modifier). Add an empty and set this as the mirror object.
hope it helps