Declare the variable outside the foreach loop, then you can access it it outside the loop.

See Coping With Scoping.

use strict;
use warnings;

open (IN1, "<design_modify1.vhd") or die;    ##### Suggestion: use 3 a
+rgument form and lexical
open (IN2, "<nets.txt") or die;              #####     file handles ou
+t of habit.  It can make
open (OUT, ">output_file.vhd") or die;       #####     some types of c
+ode safer.
open (IN3, "<enabled_nets.txt") or die;      ##### open(my $fh, "<", $
+filename) or die "cannot open $filename: $!"

my @nets = <IN2>;
chomp @nets;
my @enabled_nets = <IN3>;
chomp @enabled_nets;
my $lines = "";                              ##### Defined here (I wil
+l call it (1))

while (<IN1>) {                              ##### cuddle your braces 
+or not.  Be consistent.
    #print OUT;

                                             ##### (1) should be defin
+ed here instead, for
                                             ##### the smallest scope.

    foreach my $i (0..$#nets) {
        if (s/\=\>\s+$nets[$i]\,/\=\>$enabled_nets[$i]\,/) {
            my $lines = $_;                  ##### and here (I will ca
+ll it (2))
                                             ##### Make it '$lines = $
+_' (no 'my')
                                             ##### and you will probab
+ly see your
                                             ##### expected results.
            print "done";
            print $lines;                    ##### prints the value of
+ (2)
        }
    }
    print OUT "$lines";                      ##### prints the value of
+ (1)
}

close (IN1);
close (IN2);
close (IN3);
close (OUT);
[download]

There are many other coding practice and preference annotations that I could make as well. If you wish to hear them, just ask.

It's time to stop being a leech!

We're here to help you learn, but not to do your job, nor even to do your job of educating yourself. This question clearly means you haven't read the most basic information about scoping nor about the implication of declarring variables my $var... nor -- well, you've provided too many examples of failing to help yourself to bother listing them all. A quick review of your posts says that's a consistent behavior.