Do you mean, prevent access to them from a local user on the server? Or do you mean from the Web?
I can tell you that php files are not downloadable in the sense that css or js files are. PHP files (assuming you have a block of PHP code within) are pre-parse by php and then sent to Apache. In other words, PHP code is rendered and (typically) HTML code is sent to the browser. So, it's the same as downloading an HTML page essentially.
As for the css and js pages, well, if you plan to use them in your HTML pages, the Web needs access to them. When Apache serves up an HTML page, that HTML page is read by the browser and then the browser starts grabbing image, css, and js files. It is no different from a user typing the path directly into his or her address bar.