There is nothing to it. Two files, two filehandles. For example:

my $filename1 = "f1.txt";
my $filename2 = "f2.txt";

open F1, "< $filename1" or die "read $filename1";
open F2, "< $filename2" or die "read $filename2";

# assuming the files are exactly parallel, line for line:

while (<F1>) {
  my $line1 = $_;
  my $line2 = <F2>;

  # etc.
}

close F1;
close F2;
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