I'm not certain you've removed all the infections but if you're convinced, ignore the MBAM download.
Try this:
Firstly, boot your computer to the Safe Mode menu screen. You do this by repeatedly pressing F8 as soon as you boot up. Once there, use the arrow keys to highlight Safe Mode with Networking. Continue to boot from there, by pressing Enter.
Now open your browser and copy and paste this link into the address bar and press Enter. It's a direct download for the free version of Malwarebytes' Anti-Malware (MBAM). Install it, get updates and run a full scan (still in Safe Mode):
http://www.myantispyware.com/mbam
Now open your browser and copy and paste this link into the address bar and press Enter. It's a direct download for unhide.exe. Save it to your desktop, then run it. It should restore your icons and missing files. You may now delete Unhide.exe if you wish
http://download.bleepingcomputer.com/grinler/unhide.exe
After this, try rebooting normally. If that's successful, I recommend you run another full scan with MBAM. It will detect malware that wasn't running in Safe Mode.
Hope this helps.