There are plenty of antivirus programs you can add to your Win7PE to cleanup an infected computer. Once that is done, you can easily remove for the shortcuts, using the command prompt with administrative rights. You can type del *.lnk to remove them from the root directory. To remove folder attributes that might have been changed by the virus, you can use attrib *.* -r -a -s -h /s /d all from the same command prompt. You may later wish to rehide some of those folders.