Given the incredibly vague problem statement I'll just toss out that this looks awfully like you're trying to parse some variant of XML in which case unless you have a very restricted input that you can guarantee follows a very static format trying to use regexen to parse it is probably going to cause more headaches than it's worth. Use a proper parser (e.g. XML::Twig, XML::Simple) and save yourself the trouble.

Update: And see XML::Twig and Processing Instructions for getting, erm, XML::Twig to handle processing instructions.