Reshape to delete holes and features from an object
To delete a hole or opening, Reshape a face of a hole across the entire opening by selecting Reshape tool, click on face and drag. Drag face across the entire opening and click.
To delete geometry using Reshape, select the Reshape tool, click on the face and drag the face across the entire object. Click when done.
To remove a feature that is flush against another face, select Reshape, click on face and drag. Snap to any edge of the other face and click to ensure the faces are flush.
Observe that in all cases the Reshape operation is a “Boolean” operation resulting in clean geometry.