Files or folders are cross link

When I do a scan disk on the hard disk. An error says “The following files or folders are cross link: C:\windows\application data, C:\windows\msapps”. What can I do to solve this problem?

All the programs like : MS Office, Photoshop, Visual Basic etc are gone. Everytime I want to run a program eg: windows explorer, it will say the program has perform an illegal operation.

Anyone can help?

thanks and regards,