next if -f $subdir;

##</code><code>##

next unless -d $subdir;

##</code><code>##

foreach my $subdir ( sort @subdirs ) {

chdir($dir);
next unless -d $subdir;
...

##</code><code>##

use strict;
use warnings;
use Cwd;
use File::Path qw( make_path );

my $dir = cwd();
opendir(my $dh, $dir)     or die "Unable to open directory '$dir': $!";
my @subdirs = readdir $dh or die "Unable to read directory '$dir': $!";
closedir $dh              or die "Unable to close directory '$dir': $!";

my $result_path = $dir . '/results';
make_path $result_path;
chdir $dir;

for my $subdir (sort @subdirs)
{
    chdir $dir;
    next unless -d $subdir;
    my $newdir = $result_path . '/' . $subdir;
    make_path $newdir;

    chdir $dir . '/' . $subdir;
    system("echo '1 0' | program -f methane.trr -o $result_path/$subdir/outfile.txt");
}