RemoveEmptyDirectories.cs

public static class RemoveEmptyDirectories
{
    [MenuItem("Tools/EditorHacks/Remove empty directories...")]
    public static void MenuItem_RemoveEmptyDirectories()
    {
        RemoveEmptyDirectoriesRecursive("Assets/");
    }

    private static void RemoveEmptyDirectoriesRecursive(string path)
    {       
        var files = Directory.GetFiles(path);

        var directories = Directory.GetDirectories(path);

        if (files.Length == 0 && directories.Length == 0)
        {
            if (EditorUtility.DisplayDialog("Empty Directory", "Found empty directory\n" + path + "\n\nRemove?", "OK", "Cancel"))
            {                
                Debug.LogWarning("REMOVE " + path);
                AssetDatabase.DeleteAsset(path);              
            }
        }

        foreach (var directory in directories)
        {
            RemoveEmptyDirectoriesRecursive(directory);
        }       
    }
}