After messing around with the code some more i was able to get what i wanted. Here is the code that works. Thanks MONKS!!

#!/usr/bin/perl

use strict;
use warnings;

# emailsent.txt-will contain the name of all files for whom an alert h
+as been sent
# emailtogo.txt-will contain the name of all new files for whom an ale
+rt has to be sent
my $matchfile = 'emailsent.txt';
my $outfile = 'emailtogo.txt';

my $directory = 'C:\Perl';

open(INPUT,">emailtogo.txt");
close(INPUT);


# storing all file names in the folder into an array

opendir(DIR, $directory);
my @files = grep { $_ ne '.' && $_ ne '..' } readdir DIR;
closedir(DIR);

foreach(@files){
    print $_,"\n";
}


# Build list of old files for comparison
open my $ih, '<', $matchfile or die "Can't open file, $matchfile: $!";
my @names = <$ih>;
close $ih;
chop @names;

foreach(@names){
    print $_,"\n";
}

open my $oh_tot, '+>>', $matchfile or die "Can't open file, $matchfile
+: $!";
open my $oh_new, '+>>', $outfile or die "Can't open file, $outfile: $!
+";


# Comparing the array to the names in $matchfile
for $a (@files) {
    my $found = 0;
    for $b (@names) {
        $found = 1 if $a eq $b;
    }
    print $oh_new "$a\n", if !$found;
    print $oh_tot "$a\n", if !$found;        
}




close $oh_tot;
close $oh_new;
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