2) code was a bit overly complicated - a possible re-formulation is below.

3) A positive comment: the way that you opened all the files at the beginning is a good idea. no need to do a whole bunch of work, only to find out later that for example you can't open the output file..

Code untested:

#!/usr/bin/perl -w
use strict;

my $FILE1 = "D:/Data/WES/File1.txt";  # You can use "/"
my $FILE2 = "D:/Data/WES/File2.txt";  # avoids this \\ stuff
my $FILE3 = "D:/Data/WES/File3.txt";

open(F1,'<', $FILE1) or die "Can't open $FILE1\n";
open(F2,'<', $FILE2) or die "Can't open $FILE2\n";
open(F3,'>', $FILE3) or die "Can't open $FILE3\n";

#F3 header goes here

my %File2Parts;  # why call it F1parts? these numbers are
                 # coming from file 2. names matter.

while (my $PartNumber = <F2>) 
{
    chomp $PartNumber;
    next if $PartNumber =~ /^\s*$/;      # skip blank lines 
                              # often a "unseen" trailing blank line
                              # can cause troubles
    $File2Parts{$PartNumber} = 1;
}
    
close F2;

while (my $uline = <F1>) 
{
    chomp;  #you need this when splitting on other than white space
    
    my @ufields = split(/\|/, $uline);
        
    my ($PartNumber, $Std_Cost, $Last_Paid_Price,
        $Qty_In_Stock, $Moto_Preferred_Part, $Rev,
        $Agile_Description) = (@ufields)[0,1,2,3,7,9,10];
        
    if ($File2Parts{$PartNumber}) 
    {   
        print F3 "$PartNumber|$Std_Cost|$Last_Paid_Price|$Qty_In_Stock
+|$Moto_Preferred_Part|$Rev|$Agile_Description\n";
    }
}
[download]

Thanks a million to all for helpful suggestions. Dear Marshall, I made all changes as suggested. I am not getting any errors But looks like the "if ($File2Parts{$PartNumber})" is not working as expected. If I put the "print F3 ..." line outside the if condition it is writing File3. Any ideas? Here is my modified code:

#!/usr/bin/perl -w

use strict;

my $FILE1 = "D:/Data/WES/File1.txt";  # You can use "/"
my $FILE2 = "D:/Data/WES/File2.txt";  # avoids this \\ stuff
my $FILE3 = "D:/Data/WES/File3.txt";

open(F1,'<', $FILE1) or die "Can't open $FILE1\n";
open(F2,'<', $FILE2) or die "Can't open $FILE2\n";
open(F3,'>', $FILE3) or die "Can't open $FILE3\n";

#F3 header goes here

my %File2Parts;  # why call it F1parts? these numbers are
                 # coming from file 2. names matter.

while (my $PartNumber = <F2>) 
{
    chomp $PartNumber;
    next if $PartNumber =~ /^\s*$/;      # skip blank lines 
                              # often a "unseen" trailing blank line
                              # can cause troubles
    $File2Parts{$PartNumber} = 1;
}
    
close F2;

while (my $uline = <F1>) 
{
    chomp $uline;  #you need this when splitting on other than white s
+pace
    
    my @ufields = split(/\|/, $uline);
        
    my ($PartNumber, $Std_Cost, $Last_Paid_Price,
        $Qty_In_Stock, $Moto_Preferred_Part, $Rev,
        $Agile_Description) = (@ufields)[0,1,2,3,7,9,10];
    
    # print F3 "$PartNumber|$Std_Cost|$Last_Paid_Price|$Qty_In_Stock|$
+Moto_Preferred_Part|$Rev|$Agile_Description\n";
        
    if ($File2Parts{$PartNumber}) 
    {   
        print F3 "$PartNumber|$Std_Cost|$Last_Paid_Price|$Qty_In_Stock
+|$Moto_Preferred_Part|$Rev|$Agile_Description\n";
    }
}

close F1;
close F3;
[download]

Well something is wrong with if ($File2Parts{$PartNumber}) That statement checks for "truthfullness" of the value of that hash key's value.

Add: use Data::Dumper; at the top of the code. Then before the F1 loop, print Dumper \%$File2Parts; That will show you what is actually in the hash table. Data::Dumper is a "core module" meaning that it is already "pre-installed" in Perl. Look for spaces or other characters that would cause the hash key from file2 to not compare with the PartNumber from file1.

Of course use some abbreviated files for testing otherwise you will get a lot of output that is not helpful!

First, you can shorten your code just a bit by removing the use of $_.

while (my $ptfkey = <F2>)
[download]

The regex where you read in file 2 has a couple of issues. First, it forces start and end of line matching (^ and $, respectively). Next, it only matches the pipe and the whitespace on either side of it, so it will only match lines with ' | \n'. Lastly, it deletes everything that it matches.

If you only need to identify information in the first column, you only need to do this:

while (<F2>) {
    $ptfkey = $_; # you can skip this using above suggestion
    $ptfpn = $ptfkey; # don't need this if just matching

    $ptfpn =~ m/^(\w+)/; # if only letters and numbers
    $ptfpn =~ m/^([\d\-\.]+)/; # if it's a float
    $F1hash{$1} = 1;
    }
[download]

Secondly, the line that checks for the value should be throwing you an error:

if ($PartNumber =~ $Flhash{$PartNumber}) {
[download]

(Or, there are some languages that treat '=~' as a negation, kind of like '!=', so it could just be a typo.)

All you need to do is check to see if the value exists in the hash we created above:

if (exists $F1hash{$PartNumber}) {
[download]

Hope this helps.

Edit: I also just realized you declared %F1hash twice -- you should add the following to your code:

#!c:\perl\bin\perl -w
# note the addition of the -w

use diagnostics;
use strict;
[download]

The regex where you read in file 2 has a couple of issues. First, it forces start and end of line matching (^ and $, respectively). Next, it only matches the pipe and the whitespace on either side of it, so it will only match lines with ' | \n'. Lastly, it deletes everything that it matches.

The pipe character, if un-escaped means "or" in a regex. This regex would delete the white space in a line containing only white space - not too useful. I don't see that /g does anything. Not sure what the OP wanted to happen. But you are right, this almost assuredly not it.

$F1hash{$ptfkey, $ptfpn} = $ptfpn;

I think you just want $F1hash{$ptfpn} = 1; here.