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: $count\n";
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($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,
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