Interesting.
The fills created are not identical. They are all AIR SPACE. but the fill pen differs. Merge will combine if they use different outline pens, but not if the fill pen is different.
This difference creates the faceting of the curved edge of the log.
You would still need to select fills log by log, change the fills that comprise each log to be the same and then merge... pain in the you know what.
Note also that the line-work comprising the edge of the logs on the ends are several short lengths...
Why again were you wanting to do this?
Erika
Architect, Consultant
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"Implementing Successful Building Information Modeling"