Thank you I figured it out. I didn't even think about using a hash but what you said is a good rule of thumb.

#!perl
use Text::CSV;

$file1 = 'Master Sched.csv';
$file2 = 'Devices_01-03-2009-09-00-00.csv';
$csv = Text::CSV->new();

open IN1, "<"."$file1" or die "Can't open input file >$file1<\n";
while(<IN1>){
    chomp;
    $csv->parse($_);
    @subIn = $csv->fields();
    $agentName{$subIn[1]} = $_;
    $IP{$subIn[2]} = $_;
    $hostName{$subIn[3]} = $_;
    $product{$subIn[4]} = $_;
    foreach $x ( $agentName{$subIn[1]} ){
         #print "$agentName{$subIn[1]}\n";
    }
}
close IN1;
open OUT, ">>"."$file1" or die "Can't open output file >$file1<\n";
print OUT "\n";
print OUT ",Differences\n";
open IN2, "<"."$file2" or die "Can't open input file >$file2<\n";
while ($in2 = <IN2>){
    if($in2 =~ /Agent Name/){ next; }
    @subFlds = split(/,/, $in2);
    if($in2 =~ /\d+\.\d+\.\d+\.\d+/ || $subFlds[2] ne ''){
        chomp $in2;
        $subFlds[1] =~ s/^\s+//; $subFlds[1] =~ s/\s+$//;
        
        $w = $agentName{$subFlds[0]};
        $x = $IP{$subFlds[1]};
        $y = $hostName{$subFlds[2]};
        $z = $product{$subFlds[3]};
        #print "$in2\n";
        #print length($w)."w\n";
        #print length($x)."x\n";
        #print length($y)."y\n";
        #print length($z)."z\n";
        
        if(length($w) > 0  && length($x) > 0  && length($y) > 0){
            $csv->parse($IP{$subFlds[1]});
            @subFlds = $csv->fields();
            #print "$in2\n";
        }else{
            print OUT ",$in2\n";
        }
    }
}
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