I would like to know how to encrypt the
Encrypting the directory is not possible, but you could encrypt the underlying filesystem. However, anyone logged in with enough permissions to view the contents of that directory is still able to view files in it.
You're better off setting correct permissions for this directory, so that it doesn't include other employees/users rights.
So for example, if your FTP directory is in /home/ftp. Ensure it is only accessible by the ftp user (assuming 'ftpusr' is a valid user and 'ftpgrp' is a valid group)
# chown ftpusr:ftpgrp /home/ftp # chmod 750 /home/ftp
This way only the user 'ftpusr' and all users belonging to the 'ftpgrp' group are able to view the files inside the directory.