This is assuming the files have the same amount of lines:

use IO::File;

$f1 = new IO::File "< file1";
$f2 = new IO::File "< file2";
$f3 = new IO::File "> file3";

while (my ($c1, $c2) = map { m/^.*?\|(.*)\|$/ } ($f1->getline, $f2->ge
+tline))
{
  print $f3 "A$.|$c1|$c2|\n";
  last if eof;
}
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Reads in one line from each file, extracts the column values using map and a regex, and then prints out a new line containing both column values, plus a header made from $.