Residual Ubuntu partitions preventing disc cloning, how to remove?

Question

In my BIOS screen under boot priority, my primary (and until today only) hard disk shows up as two separate disks named ubuntu. This isn't the case when I'm just using windows, and I've never thought much of it. However, now that I've gotten a new hard drive and tried to clone the old one, there's a conflict between the two formats that I've been encouraged to fix by the cloning program. I plan on making my new hard drive a boot drive and keeping the old one for storage. How can I fix these persistent hidden partitions? I'd be willing to do some kind of linux live CD spiel if it would help, seeing as I've got a memory stick free from the cloning utility.

TL;DR How do I ensure that my hard drive is entirely Windows format and has no traces of a past ubuntu system? Basically just a hard drive with no partitions beyond what is default for the windows operating system.

Disk Manager Screenshot:

Answer 1

Given the screenshot I would recommend you to manually prepare your new disk and then clone only System Reserved and Storage (which I assume is where system is installed) partitions to your new disk using some utility that works in Windows. Try Macrium or EaseUS or something like that.

Anyway use DISKPART from command prompt to create 100MB primary partition with 1024KB offset, that is your System reserved. Next create your system partition and clone your Windows installation to it. Basically you are trying to mimic the default installation. Your cloning utility should take care of boot flag, but if not you can set it manually.

Here is how to use DISKPART.

OK if everything is good so far you should have an unbootable system now.

Now remember that offset? That is where your bootloader goes. I suggest plugging only your new disk in and repairing the bootloader using Windows installation disk.

Here is how you do it.

Be warned that this is very tedious work, so you might consider a fresh Windows install, it might be less of a hassle if you don't have a lot of programs or customization installed...