System cannot find the file specified. (0x80070002)

Newbie here...have an Acer Aspire 6930 laptop that was hit with Malware yesterday. Been slowly piecing it back together to the point that I can now logon here for help.

Issue at this point - Each time I download any "fixes" I am unable to open the file (Run as Administrator/or not) and receive the following messages:
-- "The system cannot find the file specified. (0x80070002)", or
-- "Windows cannot find 'C:\Users\...\*.exe'. Make sure you typed the name correctly, and then try again."

I have gone to Control Panel/Windows Update and hit a wall with the same error message. I have 1 update that continues to Fail to update with the same (0x80070002) error message.

Note: In my "Data D" Drive I found 11 new folders, all duplicates, all containing only these same application files in them: "mrtstub" and "mrt" in 10 folders and "checksur", "checksurlauncher", "$shtdwn$.req", "checksurpackage.ddf" in another...???

Any help/suggestions would be greatly appreciated!

Before anything else, download this and run scan. I bet it finds more malware.

Malwarebytes.org

thanks richc46, tried to "Run" vs. "Save" because each previous time that I tried to Open a downloaded patch/file/.exe, my laptop would give me an error.

This time it came up with the following message:

"ShellExecuteEx failed; code2. The system cannot find the file specified."

Did you try a repair with the Vista CD?