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I have 2 cylinders where I make a difference with boolean modifier. After applying, I see in the Edit mode that there are 2 edges connecting the outsite with the inside. Is there a way to avoid this or to join the separate faces?

enter image description here

thanks

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    $\begingroup$ Title sounds painful. $\endgroup$ – Owen Mar 11 '16 at 22:28
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If you want to convert that Ngon into quads delete it and use Ctrl+E > Bridge Edge Loops; it should work nicely if amount of vertices is the same.

bridging cylinders

However you can use more convenient way in order to construct cylinder like on your screenshot.

  1. Start with simple cylinder, select its top and bottom faces (Ngons) and inset them. Press I and drag the mouse to change effect.
  2. With both Ngons still selected use Bridge Edge Loops.

insetting cylinder inside of another one

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No, you cannot keep the Boolean Modifier from behaving like this ;-)

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