If it was my script, I'd write it like this:

#! /usr/local/bin/perl -w

use strict;

die "Not enough params!!!\n" if @ARGV < 3;

my ($input, $output, $length) = @ARGV;

open INPUT, $input or die "unable to open $input: $!\n";
open OUTFILE, ">$output" or die "unable to open $output: $!\n";

my $count = 1;

while (<INPUT>) {
  chomp;

  ++$count if />/;

  if (length >= $length)
    print ">$count\n$_\n\n";
    print OUTFILE ">$count\n$_\n\n";
  }
}

close INPUT;
close OUTFILE;
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--
<http://www.dave.org.uk>

"The first rule of Perl club is you do not talk about Perl club."
-- Chip Salzenberg