Try going to C:\Windows
If you can, Windows is on C: and it won't be affected by formatting D:
If you want to double check, enable 'show hidden and system files/folders' under 'folder options' and look in the D: root folder - if theres nothing in there, there's nothing on the drive.
I wouldn't pay too much attention to the 'filespace remaining' indicator, they're not wonderfully accurate. Particularly if you emptied D: by manually deleting stuff, the indicator is probably showing as 'used' space which is actually ready to be overwritten.