Windows Cant "see" linux partitions, but he can manage them trought Disk management console cant he?
So wizle, if you wanna formatt the linux partition point the mouse to:
Start
Right click in My computyer
Manage
Disk Management
Click in partition that Ubuntu is and format it for NTFS (thats the best one).
choose all the defaults in formatting and make sure you have the option Quick formatt enabled.
Hope that helps