I have 2 objects a face and an ear. Mirror modifier works fine for the face. But when I use mirror modifier to duplicate the ear on X axis, it duplicates on Z axis. And when I use mirror modifier on Z axis it mirrors on X axis. How to correct the axis orientation?

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If the ear was rotated, you will need to apply the rotation. To do this, in object mode either press
CtrlA then R or click Object > Apply > Rotation.
See: Why is it important to apply transformation to an objects data?
CtrlA>R. – Jan 10 '15 at 13:06