[ { is a reference to an (anonymous) array of references to (anonymous) hashes. However, in the second snippet, you use it as a reference to a hash.

Anyway, the missing magic is Text::CSV and a hash slice.

use strict;
use warnings;

use Text::CSV qw( );

my $csv = Text::CSV->new();

open(my $fh_in, '<', 'input.txt')
   or die("Can't open input.txt: $!\n");

while (<$fh_in>) {
   $csv->parse($_)
      or die("Incorrectly formatted line ($.)\n");

   my %Employee_Rec;
   @Employee_Rec{qw(
      Emp_No
      Emp_Lname
      Emp_Fname
      Emp_SSN
      Emp_DOB
      Emp_aka
   )} = $csv->fields();

   print "$Employee_Rec{Emp_No}     \n";
   print "$Employee_Rec{Emp_Lname}  \n";
   print "$Employee_Rec{Emp_Fname}  \n";
   print "$Employee_Rec{Emp_SSN}    \n";
   print "$Employee_Rec{Emp_DOB}    \n";
   print "$Employee_Rec{Emp_aka}    \n";
}
[download]

Update: If you really did want to use field indexes,

use strict;
use warnings;

use Text::CSV qw( );

my $csv = Text::CSV->new();

my %Employee_Field_Idx_Lkup = (
   Emp_No    => 0,
   Emp_Lname => 1,
   Emp_Fname => 2,
   Emp_SSN   => 3,
   Emp_DOB   => 4,
   Emp_aka   => 5,
);

open(my $fh_in, '<', 'input.txt')
   or die("Can't open input.txt: $!\n");

while (<$fh_in>) {
   $csv->parse($_)
      or die("Incorrectly formatted line ($.)\n");

   my @fields = = $csv->fields();

   my %Employee_Rec;
   @Employee_Rec{keys %Employee_Field_Idx_Lkup}
      = @fields[values %Employee_Field_Idx_Lkup];

   print "$Employee_Rec{Emp_No}     \n";
   print "$Employee_Rec{Emp_Lname}  \n";
   print "$Employee_Rec{Emp_Fname}  \n";
   print "$Employee_Rec{Emp_SSN}    \n";
   print "$Employee_Rec{Emp_DOB}    \n";
   print "$Employee_Rec{Emp_aka}    \n";
}
[download]

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