Thank you hbm for your great tips. Here is the code and output that I get for a sample record. My question was how can I eliminate the second phrase ("at the time") from the output since there is no mapping available for that phrase. 

#!/usr/bin/perl
use strict;
use warnings;
 
my $file = "regular.txt.out";
open my $fh, "<", $file or die "Unable to open $file: $!";
my($u_value, $p_value, $mc_value) = (undef) x 3;
 
while (my $line=<$fh>) {
    chomp $line;
    if ($line=~/\n\n\n/){
        ($u_value, $p_value, $mc_value) = (undef) x 3;
 
        print "\n";
    } elsif ($line=~/\bProcessing\s/) {
       $line=~s/\bProcessing\s\d+\.tx\.\d+: //;
       $u_value = $line;
        print "\n$u_value\n";
        undef $p_value;
    } elsif ($line=~/\bPhrase/) {
        $line=~s/\bPhrase: //;
        $line=~s/\"//g;
        if ($p_value) {
        print "\n" . ' ' x length $u_value;}
        $p_value=$line;
        print "\t$p_value";
        undef $mc_value;
     } elsif ($line=~/\s\s/ ) {
        if ($mc_value) {
        print "\n\t" . ' ' x length $p_value;}
        $mc_value=$line;
        print "\t$mc_value";
       } else {
     }
}
close $fh;

[download]

sample text for process

Processing 00000000.tx.3: Pulmonary embolism at the time of hip replacement

Phrase: "Pulmonary embolism"
Meta Mapping (1000)
(\s\s)1000 D0076131:PULMONARY EMBOLISM Disease or Syndrome

Phrase: "at the time"
Meta Candidates (0): <none>
Meta Mappings: <none>

Phrase: "of hip replacement"
Meta Mapping (1000)
(\s\s)1000 D0554893:HIP REPLACEMENT (STATUS POST HIP REPLACEMENT) Finding

output of the processd block is:

Pulmonary embolism at the time of hip replacement
<tab>Pulmonary embolism<tab>1000 D0076131:PULMONARY EMBOLISM Disease or Syndrome
<tab>at the time
<tab>of hip replacement<tab>1000 D0554893:HIP REPLACEMENT (STATUS POST HIP REPLACEMENT) Finding

In reply to Re^2: tab delimited extraction, formatting the output by zzgulu
in thread tab delimited extraction, formatting the output by zzgulu

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