My wife’s ancestral data is part of my tree. She wants to do her own independent research which is fine by me.
How do I produce a new RM file with just her families data on it?
As I recall splitting a database can be problematic, particularly if there are generations both above and below the person you want to split from or if there are links above the split person (cousins marrying, etc).
Might it not be better to give your wife a copy of your database that she can rename and work on independently; or that you could both work on separately but collaboratively?
Just a thought.
to this point – I am related to several people in my wife tree that she does not have a bio relationship with. He sister inlaw and uncle by married are both 7 cousins to me are two examples. If my wife left me out this would be hidden. I think most people do not realize that are often many unexpected cousins to be found between couples or other married couples or are married cousins (often 3rd cousins or closer).
Drag n drop between databases is a good option for splitting. If your database is connected to an Ancestry tree she will need to disconnect her tree from it, under Settings, WebHints, Disconnect from Ancestry tree. Then she can upload her own Ancestry tree.
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This might be and IMPORTANT CALL OUT
I think I had forgotten about that.
As Renee says, you can Drag and Drop into a new database BUT what you want to do is disconnect you from your parents— that way you can move, you the kids, her and her ancestors UNLESS she doesn’t want you as in you have no kids 
You also have to decide if you want to keep your file or if you want just one for your family
After that you MIGHT want to clean up places etc