@alldir = finddir("$config{home}$user{site_id}"); 
print "@alldir";

sub finddir {

   $root = shift;
   chomp ( $root );
   $root = $root . '/' unless ( $root =~ m|/$| );
   local *DIR;
   opendir ( DIR, $root );
   my @userfiles = sort grep !/^\.\.?\z/, readdir DIR;
   foreach $file (@userfiles) {
       next unless ( -d "$root$file" );
       $dir = "$root$file";
       $dir =~ s/^\Q$config{home}$user{site_id}\E//;
       push(@direct, $dir);
       finddir("$root$file");
   }
   return "@direct";
}
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First off, Use strict warnings and diagnostics. It'll make debugging a lot easier.

Secondly, try removing the        finddir("$root$file"); from within the foreach loop. You're exiting the loop after the first iteration.

Update: Oops. Read that wrong. Hang on a sec.

Update 2:

my %config = ( home => '/home/cjf/' );
my %user   = ( site_id => 'code'    );

my @alldir = finddir("$config{home}$user{site_id}");
print $_, "\n" for @alldir;

sub finddir {

   my $root = shift;
   chomp $root;
   $root = $root . '/' unless ( $root =~ m|/$| );
   local *DIR;
   opendir DIR, $root or die $!;
   my @userfiles = sort grep !/^\.\.?\z/, readdir DIR;
   my @direct;
   foreach my $file (@userfiles) {
       next unless ( -d "$root$file" );
       my $dir = "$root$file";
       $dir =~ s/^\Q$config{home}$user{site_id}\E//;
       push(@direct, $dir);
   }
   return @direct;
}
[download]

That will return all directories in $config{home}$user{site_id} but not go into the sub directories. Is that what you're looking for?

no I want to return all the direcotries is $config(home)$user{site_id}

The reason it only prints out one directory is that you are not pushing the results of your recursive calls to finddir into the @direct array.

       next unless ( -d "$root$file" );
       $dir = "$root$file";
       $dir =~ s/^\Q$config{home}$user{site_id}\E//;
       push(@direct, $dir);
       push(@direct, finddir("$root$file"));
[download]