my $string = '"foo"';
   $string =~ s/\"(.*?)\"?/$1/;

print $string;
[download]

But the .*? always gobbles up the trailing "

Actually it doesn't. Your non-greedy .*? matches as few characters as possible: Zero. Then, one or zero " follows. You can see it from the following snippet:

my $string = '"foo"';
   $string =~ s/"(.*?)"?/_$1_/; # note that you don't have to escape "

print $string; # prints __foo"
[download]

For a solution to your problem, see the other posts.