こんなんでどうでしょ

@echo off
setlocal enabledelayedexpansion

rem ==========
rem ｺﾋﾟｰ元↓
rem ==========
set FROM=c:\hoge

rem ==========
rem ｺﾋﾟｰ先↓
rem ==========
set DEST=c:\copy

call :COUNT %FROM%
if not exist "%DEST%\*" md "%DEST%"
call :COPY "%FROM%"
for /F "delims=" %%D in ('dir/b/a:d/s "%FROM%"') do call :COPY "%%D"
goto :EOF

:COPY
set FOLDER=%~1
set TOFOLDER=%DEST%!FOLDER:~%COUNT%!
if not exist "%TOFOLDER%\*" md "%TOFOLDER%"
for %%F in ("%FOLDER%\*.*") do copy nul "%TOFOLDER%\%%~nxF"
goto :EOF

:COUNT
set STR=%*
set COUNT=0
:LP
if "%STR%"=="" goto :EOF
set /A COUNT=%COUNT%+1
set STR=%STR:~1%
goto LP

http://d.hatena.ne.jp/papermelt/20110919/1316404963
何故かURL必須だったのでとりあえず作る時に見たﾍﾟｰｼﾞを