#!/usr/bin/perl -w
use strict;

my @header = ('h1','h2','h3'); # I already know the headings
my %values; # make a hash of hashes to remember the values

while (<DATA>) {
  chomp;
  my @columns = split /\|/;
  my $unique = $columns[1]; # h2 is the unique identifier
  @{$values{$unique}}{@header} = @columns;
}
__END__
val1|one|1
val2|two|2
val3|three|3