Just for the sake of TMTOWTDI try:

substr($files[$i],0,length($conf{rootdir})+1,'');
[download]

- or -

substr($files[$i],0,length($conf{rootdir})+1) = '';
[download]

- or -

$files[$i] = substr($files[$i],length($conf{rootdir}));
[download]

TGI says moo