Here is the base of one of my trees. As you can see, things are a bit of a mess. I am pretty sure that now is not the time to mess with this, but once the tree goes dormant is there a way to separate this guy into multiple trees?
 
Thanks for the help

Unless this was multiple cuttings or trees in a hole, it is all attached underground. You could dig the whole thing up when it goes dormant and separate the various limbs with their associated roots, then replant the trees. An easier method is to stool layer the trunks you want to move. Cut the bottom out of buckets (3-5 gallon should work nicely), slip them down the trunk to the ground, fill with dirt or growing mix, and water through the season. When the tree is dormant, separate the trunks at or below ground level and plant.

The only caveat I can think of, is any part of the trunk you leave below the soil will branch out again.

I would not attempt to separate the trunks since they are so large.  You could cut off the 2nd trunk from the right since it looks like it is rubbing against the far right trunk and leave 3 trunks.  It's hard to tell about pruning more from the picture.

Todd, Air-Layer the one that is separate from the group by placing a big bucket right underneath the trunk and slide the trunk in it then close the side with tape and fill with potting mix... before that cut a cambium ring out from the trunk, that's where the roots are going to develop... I suggest you watch few Youtube clips on air layering.
This way you can safely move the entire tree with new roots and plant it wherever you want.
There is a three created by a fellow forum member on "air layering Greek style" subject... you might benefit from talking to him also.
Good luck.

Hey Todd, I don't see anything wrong with multiple  trunks. Mine had 4 like yours and produced amazing figs, I finally got tired and took several airlayers from one of the trunks,  first small ones, then medium sizes and finally the big trunk... All replanted and doing well until the winter. Upon inspection this Spring, I see that several of them succumbed to Gnats and cold, not enough strong roots to support the upper growth..so, if I were you, don't airlayer all, or you will end up with nothing if your luck is similar to mine...but work one trunk at the time.

You could dig a little and see what the root system is. Also you can tie the side ones down so there is more air flow in the middle.
  Best luck.

I was mostly interested in the one on the far right. I don't mind the multiple branches on the main, but the one on the right is basically a completely seperate tree. There should be plenty of room to get something around the base and try to get some roots going. I planed to cut the whole thing off anyway so if it doesn't work out I haven't really lost anything,  but if I get a new tree out of the deal all the better.

Just for more info, this was one little cutting that got a fungas (I believe it was fungal at least). The tips turned black and the tree started to "dry up" towards the base. I pruned it way back and the next season it started growing from all over the place, so all of these are shoots from the original cutting. 

Hi tebmus97,
Right now the one on the right is safe to remove with a saw and a shovel but I would do it quickly to avoid big heats .
Water the dirt during three days to get it soft and sticky and go for it .
You'll have to water the new tree a bit more during the first season, but then she will rock.
I had the same case but mine where 7 trunks. I had to wait for them to grow, and in September I sew in the dirt to tare 3 apart .
And now they are 3 new trees. They had a hand full of roots when I tared them apart and still all did it.