You can nuke whole directory or sub-directory tree by using rm -rf command with -rf flags under UNIX or Linux. But ftp server does not gives rm -rf command. For ftp server you use the rmdir command to remove a directory (and rm for files). Depending on the remote server, you may be able to remove a non-empty directory.(most remote ftp server disables this option)

For example, consider my following ftp directory server structure (I do not have ssh access to this FTP box):

ccbackup/
ora9backup/
usershotdata/
vivek/
  |-Junk
  |-mp3
  |-02/09
  |-03/09
  |....
...
linux-iso/
openbsd-ports/
freebsd-ports/
tosbackup/
cnowbackup/
...

Now let us say I want remove all files and sub-directories under /vivek/ directory. There are least 100 subdirectories and deleting all files and directory manually will take lots of time.

To nuke a vivek/ directory, you need to use ncftpls command to obtain the list of all subdirectories:
$ ncftpls -u vivek -p mypassword ftp://array05.wan.nixcraft.com/vivek/

Output:

Junk/  mp3/ 02/09/ 03/09/   ...

Where,

• -u vivek : FTP login username
• -p mypassword : Ftp password
• ftp://array05.lan.nixcraft.com/vivek/ : Ftp server name (array05.wan.nixcraft.com) followed by path (/vivek/).

Now you can store a list of all sub-directories in a shell variable called LIST. Type the following command at shell prompt:
$ LIST=$(ncftpls -u vivek -p mypassword ftp://array05.wan.nixcraft.com/vivek/)
$ echo $LIST

Output:

Junk/  mp3/ 02/09/ 03/09/ ….

To remove all sub-directories from /vivek/ dir you can write a shell script as follows:
LIST="$(ncftpls -u vivek -p mypassword ftp://array05.wan.nixcraft.com/vivek/)"
for dir in $LIST
do
rdir="/vivek/${dir}"
ncftp -u"vivek" -p"password" array05.wan.nixcraft.com <<EOF
cd $rdir
rm *
rmdir $rdir
quit
EOF
done


How it works?

1. ncftp ftp client login to my ftp server.
2. Script will change directory to $rdir
3. First, it will remove all files
4. Next, it will remove subdirectory
5. And ftp connection will terminated
6. The entire cycle is repeated using a shell for loop construct.

You can obtain complete working and generic version here. You can use logic presented here to write a shell script for sftp server. You can modify this script rotate ftp backups and much more.