Your comment rightly indicates the second if is almost the same as the first one. Usually, one would abstract the common behaviour into a subroutine. Using the name OUTPUT for an input handle is a bit confusing, too (and lexical filehandles are safer than barewords). Here's my take:

#!/usr/bin/perl
use warnings;
use strict;


sub process_column {
    my ($patient, $column, $fh_out) = @_;
    if ($column =~ m/\[R\]/) {
        if (my @vars = $column =~ m/\](.*?)\[/g) {
            for my $var (@vars) {
                if ($var !~ /^\s+$/g) {
                    print {$fh_out} "$patient || $var\n";
                }
            }
        }
    }
}


open my $OUTFILE, '<', 'C:/Scripts/TEST/History21.txt'
    or die "Could not open source file. $!";
open my $NEW_MED, '>', 'C:/Scripts/TEST/History_MED1.txt'
    or die "Could not open target file. $!";
open my $NEW_SUR, '>', 'C:/Scripts/TEST/History_SUR1.txt'
    or die "Could not open target file. $!";

my $count = 1;
while (my $line = <$OUTFILE>) {
    my @rows = split /\|\|/, $line;
    process_column($rows[0], $rows[1], $NEW_MED);
    process_column($rows[0], $rows[2], $NEW_SUR);
    $count++;
}

close $NEW_SUR or die "Cannot close target file: $!";
close $NEW_MED or die "Cannot close target file: $!";

print "COUNT: $count\n";
[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]

Awesome!! Thank you!! Thank you for the explanation and solution.

First, in the for loop of the second block I think you should use $var2 instead of $var in the if condition. The Perl compiler told me this after I inserted

use strict;
use warnings;
[download]

Second, the g modifier in the second block

    if ($rows[2] =~ m/\[R\]/g) {
[download]

If I change your script to

use strict;
use warnings;

open (OUTFILE, "< History21.txt") or die "Could not open source file. 
+$!";
open (NEW_MED, "> History_MED1.txt") or die "Could not open med file. 
+$!";
open (NEW_SUR, "> History_SUR1.txt") or die "Could not open sur file. 
+$!";
  
my $count2 = 1;
while (my $line = <OUTFILE>) {
    my @rows = split(/\|\|/, $line);
    if ($rows[1] =~ m/\[R\]/g) {
         if ((my @var)= $rows[1] =~ m/\](.*?)\[/g) {
             foreach my $var (@var) {
                 if ($var =~ /^\s$/g) {
                     #DO NOTHING SINCE WE ONLY WANT IF THERE IS ANYTHI
+NG INSIDE THE 2 R BRACKETS
                 }             
                 else {
                     print NEW_MED "$rows[0] || $var\n";
                 }
             }
             
         }
      }
    if ($rows[2] =~ m/\[R\]/) {
         if ((my @var2)= $rows[2] =~ m/\](.*?)\[/g) { # I AM ASSUMING 
+IT WILL RETURN SIMILAR TO THE PREVIOUS IF STATEMENT FOR ROW1 ABOVE
             foreach my $var2 (@var2) {
                 if ($var2 =~ /^\s$/g) {
                     #DO NOTHING SINCE WE ONLY WANT IF THERE IS ANYTHI
+NG INSIDE THE 2 R BRACKETS
                 }             
                 else {
                     print NEW_SUR "$rows[0] || $var2\n";
                 }
             }
         }
      }
      $count2++;      
}
  
close(NEW_MED);
close(NEW_SUR);
[download]

ZZZZZ00DFL  || No pertinent past medical history  
ZZZZZ00DFL  || No pertinent past medical history  
ZZZZZ00C4H  || High Blood Pressure  
ZZZZZ00C4H  || Kidney stones  
ZZZZZ00C4H  || SOAPP-R Score : Moderate/High Risk:  19  
ZZZZZ00C4H  || Sleep Apnea Assessment(STOP-BANG): ( 2/4 );  7/2/2014  
ZZZZZ00C4H  || Orthotic brace tried for pain relief: Yes: limited bene
+fit  
ZZZZZ00C4H  || TENS Unit tried for pain relief: Yes: limited benefit  
ZZZZZ00C4H  || Tried Topical Compound Cream?: Yes: limited benefit  
ZZZZZ00C4H  || Acupuncture therapy tried for pain relief: Yes: limited
+ benefit  
ZZZZZ00C4H  || Chiropractic therapy tried for pain relief: Yes: limite
+d benefit  
ZZZZZ00C4H  || Physical therapy tried for pain relief: Yes: limited be
+nefit  
ZZZZZ00C4H  || Massage therapy tried for pain relief: Yes: limited ben
+efit  \
ZZZZZ00C4H  ||  \
[download]

ZZZZZ00DFL  || UNREMARKABLE  
ZZZZZ00DFL  || UNREMARKABLE  
ZZZZZ00C4H  || Hysterectomy  
ZZZZZ00C4H  || Spinal Fusion: L4-5, L5-S!; 2010  \
ZZZZZ00C4H  ||  \
[download]

Thank you! Yea I didnt know that the /g modify did that, I love this place, thanks to all the perl gurus in here for helping us newbies! Cheers!