Background:
I had installed Ubuntu 11.10 using the Windows Based installer. The idea being that if needed I would be able to uninstall easily and not deal with disk partitions, boot loaders etc.
But today when I wanted to uninstall, I saw that the Windows Program Management tool did not have “Ubuntu” as an Uninstall option.Root Cause:
Not sure how the “Ubuntu” Wubi unistaller disappeared …
But the previous install was in this mode because
(1) There was no separate Ubuntu Partition or unknown partition in the disk … checked this with dskmgr.msc
(2) I could not install the Windows installable because it said c:\Ubuntu already existed.
(3) c:\ubuntu was 19GB … implying all the Ubuntu files were stored here.

Solution:
(1) Looked in Internet and several suggestions said … Start Windows Repair Console and go to Command Prompt for bootrec.exe.

a) Windows Repair Console can be started by:

• Booting from Windows Installer CD and selecting “Repair Machine” option … OR
• Creating a “System Repair Disc” (Type “System Repair Disk” into the search box in Start option) and booting using this Disk

b) Once in the Repair Console, selected Command Prompt
c) The Boot Records can be fixed by typing bootrec.exe /fixmbr and bootrec.exe /fixboot.

But the above will not fix it. In my case the Windows 7 prompt was the default boot option and the Ubuntu was the second option. After running bootrec.exe I could still see 2 options to boot.

(2) Delete the c:/ubuntu folder and all files
(3) Now you will still see 2 options and when trying to use Ubuntu option, it will give an error.
(4) To remove the 2nd “ubuntu” option, go to Repair Console and Command prompt, type “bcdedit”.

• it will show what’s there in the boot record. The Ubuntu item will be there.
• save the contents of the Boot Manager config  — bcdedit /export bootmanager_1.txt
• now delete the Ubuntu entry … bcdedit /delete {ubuntu record’s identifier} /f

Now when you boot the Ubuntu option will not be available.