wanttoprogram:

OK, are both files sorted with respect to the key fields? If so, then you don't really want nested loops. You want a single loop and you can decide which file to read depending on what the current condition is. Something like:

# "Prime the pump"
my $rec1 = <FILE1>;
my $rec2 = <FILE2>;

# Keep looping as long as either file has records
while (!eof(FILE1) or !eof(FILE2)) {

   # Figure out what keys you have
   my $key1 = get_key_1($rec1);
   my $key2 = get_key_2($rec2);

   if ($key1 eq $key2) {
      # They're the same, so create an output record, and read
      # next record from file2
      print build_record($rec1, $rec2);
      $rec2 = <FILE2>;
   }
   elsif ($key1 lt $key2) {
      # First file has a key we don't need, just ignore
      # it and read the next record
      $rec1 = <FILE1>;
   }
   else {
      # Hmmm ... first file seemed to skip the key we need.
      # print a partial record and advance to next file2 record
      print partial_record($rec2);
      $rec2 = <FILE2>;
   }
}
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Of course, if either of the files aren't sorted on the keys, then that won't work. You'll either have to sort them, or try something like a hash table. For the hash table, you simply read the first file into a hash based on the key field(s). Then you scan through the second file, looking up values from the hash as you need them. Something like:

# Read dictionary
my %abbreviations;
while (my $line = <DATA>) {
    my ($abbrev,$longname) = split/:/, $line;
    $abbreviations{$abbrev}=$longname;
}

# Process file
open my $FH, '<', 'the_file' or die;
while (my $line = <$FH>) {
    my ($field1, $field2, $key, $field3) = split /\t/, $line;
    if (exists $abbreviations{$key}) {
        # key was abbreviated, replace with full value
        $key = $abbreviations{$key};
    }
    print "$key: ($field1, $field2, $field3)\n";
}
close $FH;

__DATA__
perl:pathologically eclectic rubbish lister
lisp:lots of irritating silly parenthesis
python:all your space are belong to us
ruby:a quack language
[download]

...roboticus

When your only tool is a hammer, all problems look like your thumb.