The above poster who recommended using the "m" flag in the regular expression is correct, however the regex provided won't quite work. When you say:
$wholeText =~ s/\"(.*)\"/$1/m; #extract the string, removed the quotes
...the regular expression is too "greedy", which means the (.*) part will gobble up too much of the text. If you have a sample like this:
"The quick brown fox," he said, "jumped over the lazy dog."
...then the above regex will capture everything from "The" through "dog.", which is probably not what you intend. There are two ways to make the regex less greedy. Which one is better has everything to do with how you choose to handle extra " marks inside your string.
One:
$wholeText =~ s/\"([^"]*)\"/$1/m;
Two:
$wholeText =~ s/\"(.*?)\"/$1/m;
In One, the regex says "start with quote, then find everything that is not a quote and remember it, until you see another quote." In Two, the regex says "Start with quote, then find everything until you find another quote." The extra ? inside the ( ) tells the regex processor to not be greedy. Without considering quote escaping within the string, both regular expressions should behave the same.
By the way, this is a classic problem when parsing a CSV ("Comma Separated Values") file, by the way, so looking up some references on that may help you out.