#!c:/perl/bin/perl.exe
use strict;
my ($file1, $file2, $file1_contents, $file2_contents,@file1_words, @file2_words, $word, $file2_new_contents);

$file1="C:/file1.txt";
$file2="C:/file2.txt";

open(FH1, "<$file1") || die "$!\n";
open(FH2, "<$file2") || die "$!\n";

$file1_contents .= $_ while(<FH1>);
$file1_contents =~ s/\s+//g;
@file1_words = split(/,/,$file1_contents);

$file2_contents .= $_ while(<FH2>);
@file2_words = split(/,/,$file2_contents);

close(FH1);
close(FH2);

foreach $word (@file1_words)
{
 @file2_words = grep {!/^\s*$word\s*$/g} @file2_words;
}

$file2_new_contents .= $_."," foreach(@file2_words);

open(FH2, ">$file2") || die "$!\n";
print FH2 $file2_new_contents;
close(FH2);