open IN, "infile.txt" or die "Error in r_open: $!\n";
open OUT, "outfile.txt" or die "Error in w_open:$!\n";
while (<IN>) {
  # do something with each line if you want
  print OUT $_;
}
close IN;
close OUT;
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This assumes "one by one" means line by line. I don't understand what you mean by "The Perl file wil then get them via <STDIN>..." Get what?