These folders have special purpose. From this article – ASP.NET Web project folder structure.
App_Code
App_Code contains source code for shared classes and business objects (for example, ..cs, and .vb files) that you want to compile as part of your application. In a dynamically compiled Web site project, ASP.NET compiles the code in the App_Code folder on the initial request to your application. Items in this folder are then recompiled when any changes are detected.
Note : You can add any type of class file to the App_Code folder in order to create strongly typed objects that represent those classes. For example, if you put Web service files (.wsdl and .xsd files) in the App_Code folder, ASP.NET creates strongly typed proxies for those classes.
Code in the App_Code folder is referenced automatically in your application. The App_Code folder can contain sub-directories of files, which can include class files that in different programming languages.
App_Data
Contains application data files including .mdf database files, XML files, and other data store files. The App_Data folder is used by ASP.NET to store an application’s local database, such as the database for maintaining membership and role information.