Here is an example with mongoose.

For each main route you must have a router.js file. Other files aren't required but a controller.js is recommended, it can be a class or a object with functions, as you want... Finally for this example there is a model.js file for mongoose, it defines my data model, the file is required in the controller.js file to manage data.
You can also use a middleware.js file to define middlewares

The api/index.js automatically import middlewares, and routes from your main route folder. In this example there is a folder named example, you can access the routes with http://localhost:4000/api/example/routeName

You have two ways to define a route; with a list or an object. An example can be found in api/example/router.js

A middleware.js file export an object with two properties, before and after, each property is a list of functions.