You are nesting your global variables. use strict; and declare them correctly. You're unnecessarily pushing your directories twice into @dir, so skip that line. Also grep only the desired files from the directory listing, adding a  grep { !/^\.\.?$/ }, which ignores "./" and "../".
This should work:

use strict;
my @dirs;
my $directory = "D:/Temp";

getdirs($directory);

for my $dir (@dirs) {
    update($dir);
}
print "DONE\n";

sub getdirs {
    my $directory = shift;
    opendir (DIR, $directory);
    my @files = grep { !/^\.\.?$/ } readdir DIR;
    closedir DIR;
    push (@dirs, $directory);
    for my $file (@files) {
        if (-d "$directory/$file") {
            getdirs("$directory/$file");
        }
    }
}
[download]

Finally, as simon.proctor mentioned, I'd really recommend using File::Find for this kind of job.


--
trust in bash
but tie your camel