if ($line =~ /^\s{0,3}(\w+)(\d+)(\w+)\s+((\w+))/)  {
   # $1-$3 used by something else here
   my $string = $4;
   {
      $string =~ s/(.{60})/$1\n/g;
   }
   print "$string\n";
}
[download]

Putting a block around it isolates the change to $1 to within that block. After the block ends, $1 will regain its previous value.

But you might be better off saving the captured items to variables right away:

if (my ($word1, $number, $word2, $string) =
      $line =~ /^\s{0,3}(\w+)(\d+)(\w+)\s+((\w+))/) {
   # $word1, $number, and $word2 used by something here
   $string =~ s/(.{60})/$1\n/g;
   print "$string\n";
}
[download]