Let's assume that you have a constraint in your application architecture that really need to be like you describe.
1. How can you secure the php address file that gets the data?
You will need to create authentication and authorization mechanisms in your php solution.
2. Parse the php file from C#
PHP generates a html file in the end, so you need to parse HTML and not PHP.
There are a great library for parsing HTML which is
HtmlAgilityPack.
JAFC