C#

private string rootpath = @"C:\FolderHierarchy\";
private string FolderSequenceCountBase = "";
private int CurrentRootPathCount = 0;
private int Counter = 0;

private void CalculateFolderHierarchyNumbers()
{
    //Get First List of Folders
    string[] Dirs = Directory.GetDirectories(rootpath, "*.*", SearchOption.TopDirectoryOnly);

    for (int i = 0; i < Dirs.Count(); i++)
    {
        FolderSequenceCountBase = (i + 1).ToString();
        CurrentRootPathCount = i + 1;
        Console.WriteLine("Processed folder '{0}'.", Dirs[i] + " = " + (i + 1));
        GetSubDirs(Dirs[i]);
    }
}

private void GetSubDirs(string item)
{
    //Get next list of folders in the folder hierarchy
    string[] SubDirs = Directory.GetDirectories(item, "*.*", SearchOption.TopDirectoryOnly);
    foreach (var DirPath in SubDirs)
    {
        //Increment count of folders within the current folder list
        Counter += 1;
        Console.WriteLine("Processed folder '{0}'.", DirPath + " = " + FolderSequenceCountBase + "." + Counter);
    }

    Counter = 0;

    //Get next list of folders in the folder hierarchy
    foreach (var DirPath in SubDirs)
    {
        FolderSequenceCountBase += ".1";
        GetSubDirs(DirPath);
    }
}