you can't remove it.  it's not really a menu either, it's a "quick search" tool.  just close it as it doesn't need to be open constantly

Set your fleet numbers then like for the first fleet set it to Ctrl + 1 or create a fleet, but using the fleet creation icons

well thanks for the answers. I knew all that, it just seems there is a lot of potential there to keep better tabs on things.

For instance, when I have a fleet tabbed, I don't need to see the fleet phasing to other planets in a seperate section on the empire tree. Just put it in Planet A or Planet B.

I like to be able to click on planets and see exactly where I have non-fleeted ships, like a colony frigate. So if I have to see that there is construction frigates, hangar defenses, repair pads, etc. etc. it may take my eyes an extra few seconds to pick out the icon for the colony frigate.  I want to unpin ALLLLL of that other crap that I have no need to click on from the empire tree. Do people really click on the empire tree to see their repair stations?

So, are there any customizable files that I can change a value from a 0 to a 1 to let me unpin some things??

Thanks for the answers.

It sounds to me like he wants to keep the planet pinned, but he wants to remove the other things from the list, such as structures he isn't going to click on or the construction ships, etc.  He just wants the planet and like the colony frigate hanging out in the gravity well.  At least that's how it seems to me.

Personally I haven't messed with the empire tree much... when it starts getting large and becoming an annoyance to the eyes I just turn it off, or collapse each planet view.  Since I usually group my ships into fleets (even single or small groups of ships) and they are at the top of the tree anyway, I can find them that way.

I haven't played online multiplayer, but I suspect you don't really have much time to mess around with the tree there.  Maybe I'll find out one day. 

Actually, in multiplayer, you probably should be using the tree quite often. It's much easier to see what kind of a threat you are dealing with in the tree than looking in the grav well. It's also very easy to queue up attack orders on specific kinds of units.

Yes, but as I said, that can't be done. The only thing you can do is increase the stack size on the empire tree to make it smaller in big games. There's no way to mod what it shows and what it doesn't, or how it works - that's all hardcoded.