Your "virtual" file could be a directory tree structure. Assuming the keys are valid names for directories, you could do something like this:

use strict;
use warnings;

my $dir = "data.tmp";
mkdir $dir unless -d $dir;
while(<DATA>){
  my( $key1, $key2, $data ) = split /\s+/, $_, 3;
  mkdir "$dir/$key1" unless -d "$dir/$key1";
  mkdir "$dir/$key1/$key2" unless -d "$dir/$key1/$key2";
  open my $fh, ">>", "$dir/$key1/$key2/data.txt";
  print $fh $data;
  close $fh;
}

opendir( my $dh, $dir );
for my $key1 (sort grep { !/^\./ } readdir $dh) {
  opendir( my $dh1, "$dir/$key1" );
  for my $key2 (sort grep { !/^\./ } readdir $dh1) {
    open my $fh, "<", "$dir/$key1/$key2/data.txt";
    while( <$fh> ) {
      print "$key1\t$key2\t$_";
    }
    close $fh;
  }
}

system( "rm -rf $dir" );

__DATA__
key1  key2  ndnjfgdsjfjjkjjfjf...
key1  key2  kdfkjdfgdfugbjndkfgkjgndkjfjkd
key43 key21 sdkjfhdghdbgbd
key1  key3  jujdejnsduhffnjj
key2  key2  jhzezhdjjf...
[download]

If things go wrong, you only have to delete the one directory... WARNING: No error checking in this code, you need to add that yourself!