Nested loops will not give you what you need. Besides Moritz's solution, you could also use one loop on one of the files (but not on the other): 

while (my $a = <F1>) {
     my $b = <F2>;
     # do something with $a and $b
}

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In reply to Re: reading two files in parallel by Laurent_R
in thread reading two files in parallel by baxy77bax

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