The Family Historian Named List functionaity is intended to provide the same kind of functionality and more that you can achieve by 'marking' individuals in other programs. Here's an example of how you can use it to do what you want to do. Create a named list and add to it all those people who you want to put into a separate GEDCOM file.
To split a GEDCOM file, you use the Split Tree Helper functionality. There's a small section on this in Chapter 13 of the User Manual. Or open the dialog (click on File > Split Tree Helper) and click on the Help button to see the Online Help on it (more info than in the User Manual). Please make sure you clearly understand how the Split Tree Helper dialog works before you use it. Bear in mind especially, that you are supposed to be working on a copy of your GEDCOM file and NOT on the original when you use this dialog (unless you definitely know what you are doing).
The Split Tree Helper file let's you use queries to specify which Individuals you want to delete from/leave in the file copy. It doesn't directly allow you to specify your Named List. However any Named List can be turned into a query effectively. All you have to do is create a custom query (for Individuals in this case), and add a list filter to add all the people in the specified named list. Then when you run that query it will include all and only the people in that named list; and you can use this query in the Split Tree Helper dialog to access the people you want - i.e. the people in your Named List. If you are likely to do this regularly you can keep both the Named List and the Query and perhaps give them a generic name (e.g. you could, if you like, use 'Marked Individuals' as the name of both the query and the Named List).
Simon Orde List Administrator and Family Historian designer