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

while (my $ptfkey = <F2>)
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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;
    }
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Secondly, the line that checks for the value should be throwing you an error:

if ($PartNumber =~ $Flhash{$PartNumber}) {
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(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}) {
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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;
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