Coming from structured framework like Rails and Symphony, Meteor does not enforce a fixed structure, if fact you can write your files anywhere, still there are conventions like the following one:
An alternative is to rely on something like Iron Generator. This CLI (npm package) creates your desired application structures (i.e. folders and files), by providing at the same time proper generators to create scaffolds for your models, controllers and views.
Here there is an example of usage of the above mentioned Iron Generator.