in reply to modifying a string in place

while (<>) {
  s/([^^#])/$1$1/g if ($. > 4);
  print;
}

[download]
or just perl -pe 's/([^^#])/$1$1/g if ($. > 4)' file > newfile
Caution: Contents may have been coded under pressure.

In Section Seekers of Perl Wisdom