The system is trying to find a program named 'rmdir /s /q'. You must write 'rmdir' instead:

 system ( 'cmd', '/c', 'rmdir', '/s', '/q', $file);

update: use cmd /c to call the "cmd" shell, which runs rmdir for you.

By the way, if you would delete files you could use perl's own  unlink() instead.

update: Albannach told me that  perldoc says:

"unlink" will not delete directories unless
you are superuser and the -U flag is supplied to
Perl.  Even if these conditions are met, be warned
that unlinking a directory can inflict damage on
your filesystem.  Use "rmdir" instead.
[download]

Use "unlink" only for deleting normal files.