How do I determine what MDF files are in use
The  Best way  to delete  databases in sql server is     using    DROP DATABASE  command .
If you right click and delete in SSMS  you will end up with files left in folder .

Then You have to manually remove the files from server folder .

To remove these files from folder , first bring sql server to online  then go the folder and start deleting  the files ,  when deleting mdf or ldf files  you will get error like files in use  means that database you are using and you can remove remaining .