You should get what you want by using binmode to create the file:

use strict;
open OUTFILE, ">binfile";
binmode OUTFILE;
print OUTFILE "1\n2\n3\n4\n";
close OUTFILE;
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This creates a file which at the dos prompt shows as having a size of 8 bytes. Hope this helps!

Update: So if you start with an existing file, try the following:

use strict;
open OUTFILE, ">binfile";
binmode OUTFILE;

open INFILE, "<CrLf";
my @lines = <INFILE>;
close INFILE;
chomp @lines;

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

close OUTFILE;
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Or read/chomp/print line by line.

"Make everything as simple as possible, but not simpler." -- Albert Einstein