Gettng 404 errors

This is my first time working with CI, I'm trying to upgrade from CI 2 to 3.1.11. I followed the instruction in the user guide and was able to get the main page to load the login screen. Anytime I try to login or click any other link (which checks to see if im logged in and redirects) I get a 404.

domain.com/application/base.php/controller/function
The page you requested was not found.