This past weekend, I had successfully moved a physical Linux box to a Windows Server 2008 R2 Hyper-V.
I thought this might have been a long and very difficult process, but is wasn't with the help of Clonezilla. I will walk you through the process that I did below.
Portable USB Hard Drive (I used a 1TB Drive)
The first step in the process was to make sure that no one was using the server and then to shut the server down.
I then booted up the computer with CloneZilla and followed the on-screen instruction under "Beginner". (I have a bootable flash with CloneZilla, if any one would like directions on how to do that, please let me know and I will post some.)
While Clonezilla was working on backing up the server, I created a Hyper-V virtual server.
Once I had an image file of the physical machine from CloneZilla, I plugged it in to the Server 2008 box.
Now, this was a tricky part for me: How do I get a Hyper-V guest to "see" a physical usb drive. This turned out to be simpler than I thought. If you go into "Disk Management" and right click on the usb drive and select "Offline", you can add it to a Hyper-V guest.
Once I added the usb drive to the guest, I booted the guest using Clonezilla ISO. From here, I followed the directions to restore the image. Once it finished, I ejected the ISO from the guest and booted the server.
Once the server finished booting, I made sure that the users could access it. The users have not noticed any difference.
I repeated this process on another server that had a raid card in it and CloneZilla had no problem with it.