I use Android File Grouping plugin for Android Studio.It doesn't really allows you to create sub-folders, but it can DISPLAY your files and resources AS they are in different folders. And this is exactly what I wanted.
You can install "Android File Grouping" plugin by
Windows:
Android Studio -> File -> Settings -> Plugins.
Mac:
Android Studio -> Android Studio Tab (Top Left) -> Preferences -> Plugins -> Install JetBrains Plugin..
For Mac, I was able to test it and was not able to search for the plugin. So I downloaded the plugin from here and used the Install plugin from disk
option from the above setting.