If You are planned to develop a project(Stand alone application/Web development) you have to look into many aspects regarding security,code readability and re-usability,understanding and many aspects as per your project goes.

What ever your project domain or what ever your technology chosen for project you will be having directory and file structure. Or else the total system will be confusing and some times the whole project concept will be clopsed. So you should be careful on directory and file structure once you finished your project requirement analysis, and another reason for security reason also you should follow a structured way of programming.

Whether you can define your own file structure or you can have already built in architectures.

If you are planned to write your own file structure means have these things in your mind.

1. Storage

2. Programming

3. GUI

Even stand alone or web application you should have these analysis.

Or if you are planned to use built in architectures means i always recommend you just know about MVC and you will be happily programming. Especially when it comes web application it supports you more than you expect.

Because it is not technology dependent. You can use it in PHP/ASP/JSP

What is MVC Architecture?

The main aim of the MVC architecture  is to separate the business logic and
application data from the presentation data to the user.

Advantages of MVC

1.Modifying isvery easier
2.Clean separation of roles
3.Easy to maintain and future enhancements
4.Parallel development
5.Gives the good productivity

Dis-advantages

1.For parallel development there is a needed multiple programers
2.Knowledge on multiple technologies are required

If you can able to manage above to disadvantages in your project means then i am sure you will be using MVC architecture.