コマンドラインから以下を実行
for /f "delims=" %d in ('dir /ad /b /s') do rd "%d"
ディレクトリを指定する場合(e:\tmp配下のディレクトリ)
for /f "delims=" %d in ('dir e:\tmp /ad /b /s') do rd "%d"
参考
http://so-zou.jp/software/tool/system/command-prompt/command/rd.htm
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