If you set the $LIST_SEPARATOR ($") variable to the empty string (it is a single space by default), your substitution will not remove a space. The array variable is being interpolated as if it were in double quotes inside s/// (see Quote and Quote like Operators):

$" = '';
$id='TEST TEST';
print "$id\n";
@filename_filter=('*','|','<','>','?','/');
$id =~ s/[@filename_filter]//g;
print "$id\n";

__END__

TEST TEST
TEST TEST
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