Hello,
I used secure delete tools (srm and sfill) to get rid of old/private files securely. After deletion and wiping free space, I checked the partition with testdisk tool. It seemed that there were remaining directories (their size is 0 and one cannot enter them as testdisk said the "file may be corrupt"). How can one delete these directories? (As I see, secure deletion would mean that nothing remains on the disk, no directory names, etc.)

An example:
sudo srm -rf .software
but after this I can see the . software directory in testdisk with size 0.

if I understood it well: the name of the dir is stored in the parent dir, therefore you need to secure delete that, or overwrite that entry (although I do not know how can one overwrite a deleted entry in a dir). Probably I would rename it before deleting its content.

You understood well.
Then, there is no way for secure deletion in this case?