Directory structure + .htaccess for a php api within a web app

I am attempting to integrate a PHP web API within an angular/html app. The root folder is called "app". It should contain both the web app (that consumes the php api), aswell as the api itself (an api call would be /app/api/v1/user/ which in turn would be consumed by the web app using AJAX).

My main issue is that when making a request within a web app's route (for instance /app/user), the server attempts to process the request as if it was part of the api. How do I separate the api from the web app while retaining the "/app/" access