Keep in mind that your assignment is totally broken. Missing equals sign aside, see what this does:

my @array = (%hash1, %hash2);

What you end up with is merely a list of the key/value pairs from %hash1 and %hash2, not an array of hashes.

As hardburn suggested, what you want is a hash of hashes (HoH):

use warnings;
use strict;

my @template;
my %data;

while (<>)
{
     chomp;

     my @line = split(/\|/, $_);

     if (!@template)
     {
          @template = @line;
     }
     else
     {
          my $key = lc($line[2]."_".substr($line[1],0,1));
          @{$data{$key}}{@template} = @line;
     }
}

use Data::Dumper;
print Dumper(\%data);
[download]

I really have no idea how you were going to name your hashes like that, so I guessed. Note that you might have to fix the $key definition so that two "B.Smith" people don't collide.