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That's not possible at this point.
Someone has just requested the feature that certain ports(uplinks) be excluded from being mapped.
(in this forum).
I've suggested it as well...the ability to pick/exclude particular ports would make this a much more useful application.
It would also be nice if you could have it set up with all your devices in you environment and be able to search for an IP or MAC address. Have it also take into account that if the link is a trunk port to keep looking until it can narrow it down to a single interface if possible.