Yeah you can do it but it'll take a little work. You can create a fictional league with however many teams and minor leagues you want (if any). Then mass delete all the fictional players and import your historical players using the mass import text file:
http://www.ootpdevelopments.com/boar...-3-0-plus.html
http://www.ootpdevelopments.com/boar...-possible.html
http://www.ootpdevelopments.com/boar...l-players.html
Then just set up a free agent draft .
Or, you could set up a quickstart using the All-Time Greatest Players QS that comes with the game and export all its rosters to a text file. Open that text file with Excel and then do the same with your fictional league rosters. Make sure you have the same number of players in each file and then copy and paste all the ATG player info EXCEPT player IDs, team IDs, and team names into your fictional league rosters. Save that file as a .csv file and then import it into your league. Then dump all the players into the free agent pool and set up a free agent draft.
In both cases, if you want historical players to keep showing up in the amateur drafts, then you can click that option in the setup but you'll have a lot of duplicate players after a while.