If so, then the Windows folder of importance is still there.. Why are you typing in D:\Windows? Are you unable to access it through Windows Explorer?
Which operating system are you using? Are you sure the D drive is the actual boot drive of the computer? Most machines have Windows on the C drive. Have you looked on the C drive for the folder?
I suspect you haven't fully removed your malware problem.. Please describe what you have done to clean up the machine.. Which tools?
Hope this helps and let us know more.
Grif
Strangelly i waked up one morning and found my WINDOWS folder gone...
my windows is installed on drive D: ... i typed in D:\windows and it worked but the folder isn`t visible even if i go to the "Show hidden files and folders" tab under folder options.
i think the problem may be a changed registry key `cuz i`ve been infected with subseven2.2A, startpage.BK trojan,Flooder.Mailspam.VB.L trojan but got the system clean out.
i also used tuneup utilities 2007 to clean the registry ... still nothing
i used a game accelerator too (i think this messed up the system)
but what can i do to make the Windows folder visible again ?

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic