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I have a simple cube which is scale and rotated. When I try to apply rotation and scale. Its get applied but why the cube rotate from its angle. It was rotated in 63 degree. After applying the rotation and scale it in the vertical direction.

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Actually your object is not a cube mesh, the box we see is the bounds you can display around your object in the viewport:

enter image description here

As you've rotated your object, it has been rotated as well:

enter image description here

If you apply the rotation, it doesn't rotate the object, that's what we are expecting, but it resets the bounds box, which is also expected for an object that has now a rotation of 000:

enter image description here

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  • $\begingroup$ Thanks . A suggestion with this file same issue. The circle disappear when apply rotation to it. <img src="https://blend-exchange.giantcowfilms.com/embedImage.png?bid=99MVMGRV" /> $\endgroup$ – atek Aug 17 '20 at 14:33
  • $\begingroup$ it has to do with your Btool_plane modifier, if you apply the rotation of Cube.001 it looks like it doesn't work anymore, I'm not sure how you made this boolean work the way it works though, did you make this object? $\endgroup$ – moonboots Aug 17 '20 at 16:40
  • $\begingroup$ Yes. and my model is almost complete. Need a backup so i dont want to apply modifiers. imgur.com/a/sbHxl3s $\endgroup$ – atek Aug 17 '20 at 16:55
  • $\begingroup$ Plane is just a plane so are you able to cut out Cube.001 this way with a Boolean, I miss something here $\endgroup$ – moonboots Aug 17 '20 at 17:51

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