It writes a line to to a specific place in an external file. Problem is each time it runs it adds another line just under the former line.

That's because you didn't remove the newline that was there. See perldoc -f chomp. And Zaxo is right, you shouldn't loop the entire array when you already know the index. Given that, the foreach loop becomes:

chomp $array[3];
$array[3] .= "my newline goes here\n";
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As fruiture already said, I propose you use Tie::File. You don't need to do all the open/read/close hoopla yourself, plus it doesn't slurp the file so it will be more efficient. That's especially important when writing CGI scripts, where usually every byte of memory and every millisecond saved counts.

Makeshifts last the longest.