Secure Delete has an internal list of files which it queues to delete. If this list overflows you will get an error message and the file will not be added to the queue ( deletion of other files will continue ). The queue limits are of 65536 files to delete and of 256 drives to clear free space on. These limits are of course only for each CLI instance of the program. Simply run another instance or run the program again to delete files which would not fit on the queue. In GUI mode you cannot select multiple files to delete. This is a limitation of the Java language. For multiple deletions it is much easier to use the CLI or to use drag and drop on the desktop.