I did not notice afoken's note until after I wrote this code, so here it is.
To do this right, you need a slightly complicated structure - a hash-of-arrays. 
#!/bin/perl -w
use strict;
use warnings;

my @filenames = ("file1.txt", "file2.txt");

my %result; # Hash of arrays

for my $fname(@filenames){
  my $currentheader = "";
  open my $f, "<", $fname or die "Cannot open '$fname' : $!";
  while (my $line = <$f>){
       chomp $line;
       next unless length($line); # Skip blank lines
       if ($line=~/NAME/){
           $currentheader = $line;
           next;
       }
     push @{ $result{$currentheader} }, $line; 
  }
}

# Print results
for my $currentheader(sort keys %result){
    print "\n$currentheader\n";
    print "$_\n" for @{ $result{$currentheader} };
}

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In reply to Re: Merge the difference between two files by NetWallah
in thread Merge the difference between two files by hopper

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