use strict;
use warnings;

...

my ($part_number, $part_desc, $company1_price, $company2_price) = (split /\t+/, $row )[0,1,3,5];

next unless $company1_price =~ /\d/ and $company2_price =~ /\d/;

$company1_price =~ s/\s+//g;
$company2_price =~ s/\s+//g;

print $company1_file, "$part_number\t$part_desc\t$company1_price\n";
print $company2_file, "$part_number\t$part_desc\t$company2_price\n";

...