If you have windows 8.1 RT, you will have to send it in for repair. If you have the regular version of Windows 8.1, you will need to get a windows 8.1 installation disk and boot from it to either repair or reinstall windows.
Files don't just go missing. Did you delete anything or attempt to do any service to your computer? If not, it could be a sign that your hard drive is failing or that you have a nasty virus.