Thank you for your help! I guess that I was not using the undef correctly? Now, when the filed in the array is blank "00:00:00" is put into the array. My code now works and looks like this:

#!/usr/bin/perl -w

use DBI;
my $dbh = DBI->connect('DBI:ODBC:PERL', {AutoCommit => 1},)
    or die "Couldn't connect to database: " . DBI->errstr;

$log = print "Enter FS log name> ";
chomp($log);

open($LogDate, ">>LogDate.txt");

while ($log = <>) {
    open(DATA,$log);
        @file = <DATA>;
    close(DATA);

    foreach $line (@file) {
        $line =~ s/"//g;
        @day = split(/ /,$line);
        $func = shift @day;

        if ($func =~ /^Initiated|^Execution/) {

            if ($day[2] =~/on/) {
                chomp($log);
                print "\n$log,$day[3],$day[1],";
                print $LogDate "\n$log,$day[3],$day[1],";
            }

            if ($day[2] =~ /terminated/) {
                print "$day[5]";
                print $LogDate "$day[5]";
            }
        }
    }

    close($LogDate);

    open(DATA,"LogDate.txt");
        @file = <DATA>;
    close(DATA);

    foreach $line (@file) {
        chomp($line);
        @array = split(/,/,$line);

########## This is where the problem was ##########
        if (length $array[3]) {
            # do nothing
        } 
        else {
            $array[3] = '00:00:00';
        }
##################################################

        $dbh->do("INSERT INTO tblLogDate (Log,Dte,Start,Stop)values('$
+array[0]','$array[1]','$array[2]','$array[3]')");

    }

    $dbh->disconnect;

    exit
}
[download]