How Can I Remove All The Commented Section From The Web.Config File Using C#?

You could do it with a Regex:

(\<!--)(.*?)-\>)

Read your file into a string, regex it, and write it back:

string data = File.ReadAllText(path);
string noComments = Regex.Replace(data, @"(\<-)(.*?)-\>)", "");
File.WriteAlText(path, noComments);

But I have no idea why you would want to remove comments: they are generally there for a very good reason...-->