Do you enter peripheral relatives? That is, do you enter parents of spouses? Siblings and nieces and nephews of spouses? Other spouses of spouses? Other children of spouses of spouses from prior or subsequent marriages? Do you follow / trace step-children?
There are two places in FTM where to export datasets:
1) File > Export
2) Publish > Charts > Right click in an open area of the chart > Choose to export all in a chart.
If you don't have peripheral relatives, you can do a "simple" export at File > Export - of ancestors only.
If you do keep track of peripheral relatives (which I believe most of us who actually research do), you will need to detach you and your wife, select one or the other, and go to Publish > Charts > Extended Family Chart, and select ALL persons, 99 generations in the right panel. Then right-click export and then right-click delete the resulting dataset. You will want to do this, of course, only after you have backed up your file so that you can recover it in case your procedure has unexpected results.
One complicating factor will be if you or your wife have cousin marriages connecting your trees in a manner where you are cousins to each other. That really complicates things if you want to separate files - in fact, the better solution would be to not separate your trees if you are cousins to each other. (ie New England ancestors.)