#!/usr/bin/perl
use warnings;
use strict;
use POSIX qw(strftime);

=for
 Will execute as a cronjob every evening @10PM.
 The "SequencingResults" dir is where the search will begin.
 The script will search subdirs based on the date.
 If the current date is " 01-16-09", then the path will
 be "SequencingResults/RESULTS 2009/JAN 2009/Results 01-16-09".
 If the first file has either LacZ|pgK|SD|SU then it will mv that file
 to $seqdir. It will do this recursively for each file.
=cut


my $topdir = "/home/mgavi/testdir1";
my @subdirs = get_sub_dirs($topdir);
my $bottomdir = strftime "Results %m-%d-%y", localtime;
# This keeps track of the current year
my $yeardir = $year
# This date will be passed readdir to get the current subdir
my $date = strftime "%m-%d-%y", localtime;
print "$date\n";

sub get_sub_dirs {
    my $dir = shift;
    opendir my $dh, $dir or die "Error: $!";
    #print "$dh\n";  #this is your glob
    my @dirs =  readdir $dh;
    #@dirs = grep /^Results(.*)$/,@dirs;
    @dirs = grep /^RESULTS(.*)$/,@dirs;
    closedir $dh;
    return @dirs;
}
print "subdirs = @subdirs\n";

foreach my $dir(@subdirs){
    opendir my $dh, "$topdir/$dir" or die "Error: $!";
    print $dh;
    my @files = readdir $dh;
    #print "raw files = @files\n";
    @files = grep /^(\d+\D\d)_(LacZ|pgK|SD|SU)$/,@files;

    #print "$dir -> @files\n";
    # create dir for raw seq files with permissions
    my $seqdir = "/home/mgavi/testdir2/SeqAssembly";
    mkdir $seqdir, 0755;
    foreach my $file(@files){
                system( "mv $topdir/$bottomdir/$dir/$file $seqdir/$fil
+e");
    }
    closedir $dh;
}
[download]

Stdout is:
01-14-09
subdirs = RESULTS 2008 RESULTS 2009 RESULTS 2007
GLOB(0x804cd08)GLOB(0x804cd08)GLOB(0x804cd08)

None of the files are being moved to the new dir.

I added File::Copy to move files.