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1. Select the Extract Entity tool. 
2. Select the Remove Open Gap mode from the Inspector bar or Local menu. 
3. Hover over the edge of the hole you wish to remove, and click on it.
   
   Result:
   

To remove an open gap with the Remove All Open Gaps option.:

1. Select the Extract Entity tool. 
2. Select the Remove Open Gap mode from the Inspector bar or Local menu.
3. Select the Remove All Open Gaps option from the Inspector bar or Local menu. Image Added
4. Hover over the object with the holes you wish to remove, and click on it.
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   Result:
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