/(\d\d\d\d.\d\d\d\d)/ will match on "/home/limo/Perl/2000/0827/test_dir", but $1 won't have what you want (the . token matches any single character except \n, but it doesn't replace it with a period). Try this.

#!/usr/ug/bin/perl -w
use strict;
use Cwd;
my $dir = getcwd;
my $date_suffix;
$dir =~ m!(\d{4})/(\d{4})! or die "In a bad directory: $dir";
$date_suffix = "$1.$2";
print "$date_suffix\n";
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