in reply to replacing string in multi-line text file

1. First of all use three argument open with exception handling like

open(my $fh, '<', "input.txt") or die $!;

2. secondly, your code is adding a new line at the bottom of the text file because you are opening a file in append mode ie., >>

use '+<' is almost always preferred for read/write updates.

For more detail see http://perldoc.perl.org/functions/open.html