app/
   build.gradle
   src
jni
AndroidManefest.xml
build.gradle
settings.gradle  
It's doable and here is how I did it:
1) Import the eclipse project from Android Studio.
   *if you have a android studio project already, skip this step.
2) Open build.gradle under sub dir app/ and copy the contents and append/paste it to build.gradle of the top level.
3) Move all files under app/ to top level.
   *if you don't have these files in top level yet.
4) Remove settings.gradle.
   * you don't need it any more since you don't have app as a submodules.
5) Added the following lines to build.gradle  
sourceSets {
    main {
        manifest.srcFile 'AndroidManifest.xml'
        java.srcDirs = ['src']
        resources.srcDirs = ['src']
        aidl.srcDirs = ['src']
        renderscript.srcDirs = ['src']
        res.srcDirs = ['res']
        assets.srcDirs = ['assets']
    }
- Change the dir name to match your layout.
 6) "Clean Projet" and "Rebuild Project"
Note:
If you have other submodules in additional to "app", you will need keep settings.gradle and remove:
   include ":app"
from it and keep other submodules.  
See my project layout here:

The final build gradle is a combination of two together:

Hope it helps.
David