Don't know what your exact problem is, but I suggest you use the 3 parameter form of open and lexical file handles as well. 
my $infile  = "/Users/me/Desktop/CCDS.current.txt";
my $outfile = "/Users/me/Desktop/withdrawndata.txt";

open my $infh, $infile or die "$infile: $!";
open my $outfh, '>', $outfile or die "$outfile: $!";

#remove the header
my $firstline= <$infh>;
chomp $firstline;

while (<$infh>){
    chomp;

    my @fields = split /\t/;

    if($fields[5] =~ m/Withdrawn/){
        print $outfh "$_\n";
    }
}

close $infh;
close $outfh;

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In reply to Re: Where is my output stream to a file going? by wind
in thread Where is my output stream to a file going? by lomSpace

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