Just use any of the many algorithms to split an array into smaller chunks. The simplest is to splice until an array is empty:

use strict;
use Fatal qw(chdir opendir mkdir rename);

chdir "...";
opendir my $dh, ".";

my @files = grep !/\A\.\.?\z/, readdir $dh;
my $index = 0;

while (@files) {
    my $dir = sprintf "images%02d", $index++;
    mkdir $dir;
    rename $_, $dir for splice @files, 0, 1000;
}
[download]

This code is dirty and untested. Don't use it unless you fully understand what it does.