Ok, looks like secondary IE's are not bound to primary, but tertiary's are bound to secondary? If so, you need to read in each primary and secondary. When you find a tertiary, you'll want to have an array (or similar) tied to that corresponding secondaryIE. Now you can sort each independently. It's more about reading in and data structures than sorting. For instance:

Semi-Pseudo-Untested-code:

 while ( <FILE> ) {
  if ( isPrimary() ) {
    push @primary, $_; 
  } elsif ( isSecondary() ) {
    push @secondary, $_;
  } elsif ( isTertiary() ) {
    push @{$secondary[$#secondary]}, $_;
  }
 }

 @primary = sort { $a cmp $b } @primary;
 @secondary = sort { $a cmp $b } @secondary;
 
 foreach $secondaryItem ( @secondary ) {
  @{$secondaryItem} = sort { $a cmp $b } @$secondaryItem;
 }
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Something like that - anyways, don't forget to use strict :)