Hi,

Please help me out to find my flaws

Please consider the following:

• It's a lot better, to use warnings; and strict; at the top of ones script
• It's modern ( ha ha... ) and a lot safer to use open 3 arugments
• Barewords as filehandles might not be too good, you can use lexical variable of your choice.
• Lastly, you will want to close, your filehandles, as soon as they are opened

Below is the reconstruct of your script.
Please, note I used regex to get what I assumed to be first column of your data used.
Using split or even substr might probabily be better, if OPs data is known. I can only assume data here.

use warnings;
use strict;

open my $fh,  '>', 'outfile3.txt' or die "can't open file: $!";
open my $fh2, '<', 'file1.txt'    or die "can't open file: $!";
while ( defined( my $line = <$fh2> ) ) {
    if ( $line =~ m{^(?<matched>.+?)\s+?.*?$}){
      print {$fh} $+{matched}, $/;
    }
}
close $fh2 or die "can't close file: $!";
close $fh  or die "can't close file: $!";
[download]

Hope this helps.