I am looking at buying a pair of big jon bird trees, does anyone know if the black base of it can be removed or, does it attach permanently to the boat? I haven't senn them in person, I don't want to have the base sticking up a few inches when the bird tree is not in place. I am not looking to mount a track system for these.

http://www.bigjon.com/store/list.asp?SubTypeID=5&ProductID=67

That looks like the same base that came with my planer mast. The base has eight mounting holes in it. I suspect the inner four holes line up with the mounting plate for a Big Jon downrigger. They have thumbscrews that attach their Downrigger to the plate. If thats the case all you need to do is permanently attach the downrigger mount which is about 3/8" thick and screw in the thumbscrews. You may be able to contact Big Jon and verify this.
Otherwise you may be able to find a local machine shop that can make a mounting plate for you. That would be very simple to make from either Aluminum or Stainless Steel.

Good Luck.