Use a hash rather than 2 loops. Format the output with printf

#/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;

my $search = 'Wood';

my %file01 = ();
my $inFile01 = "FILE01.dat";
open DATA01,'<',$inFile01
  or die "Can't open file '$inFile01' : $!";

while (<DATA01>) {
  chomp;
  # Skipping if the line is empty or a comment
  next if ( $_ =~ /^\s*$/ );
  next if ( $_ =~ /^#\s*/ );
  
  my ($county,$var,$stcode) = split ";",$_;
  if ($var eq $search) { 
    $file01{$county} = 1;
  }
}
close DATA01;
print Dumper \%file01;

my %result = ();
my $inFile02 = "FILE02.dat";
open DATA02,'<',$inFile02
   or die "Can't open file '$inFile02' : $!";
    
while (<DATA02>) {
  chomp;
  # Skipping if the line is empty or a comment
  next if ( $_ =~ /^\s*$/ );
  next if ( $_ =~ /^#\s*/ );
      
  my ($code,$attr,$county) = split ";",$_;
  if ( exists $file01{$county} ) { 
    push @{ $result{$county} },$code
  }
}
close DATA02;
print Dumper \%result;

my $fmt_1 = "L|A|%d|%d|||||||||||||||||||||||\n";
my $fmt_2 = "M|A|%d||||%s|%s|CONSTANT_STRING\n";
foreach my $county (keys %result) {
  for my $id ( sort @{$result{$county}} ){
    printf $fmt_1,$id,$id;
    printf $fmt_2,$id,$search,$search;
  }
}
[download]