Disk Storage will not clear out

I am using Backup Exec 2012.  I have 4 disk partitions that are 4.54TB each.  I have had issues with the data being dropped as being expired.  So I have to manually go to the Disk Storage in Backup Exec and click on Backup Sets and delete all the data that way.  I have always done that.  But I have noticed that even though when I do this,  there is still not the full disk storage being cleared.  I looked at the disk via Windows Explorer and there are files there (.bkf) that are old nut I am afraid to remove them.  I have read that by deleting from the disk instead of using Backup Exec delete backup sets,  that the configuration files will be messed up.

So my question is how do you remove those??  How do I get all of my storage back to use??

Thanks much

Cathy