The problem of the scorched earth solution (i.e. reformatting the drive) is that you never find the problem and as a result you’re likely going to have the same problem come back shortly after all the work of re-formatting the drive.

A simple solution is to put the infected drive in another computer, but set to be a slave drive in the other computer. Doing this means that the data is accessible without loading any programs on the drive.

Once the drive is in the other computer, run a suite of anti-virus and anti–spyware detection and removal tools. While both Spyware Doctor and Malware Bytes (mentioned above) are both excellent at detecting some spyware, they are selective in what they find. As a consequence you should use several programs. When I'm hired to do these kinds of scans, I use a total of 7 programs plus some other things. Generally all of the programs will find things the others missed.