The files that cannot be scanned have normally a .sys and .ini extension which means that they are system and registry files, for example:
C:\Users\<username>\ntuser.dat - the file that contains the user profile
C:\Users\<username>\AppData\Local\Microsoft\Windows\Usrclass.dat - a file that is part of the User Profile
C:\Windows\System32\config - this contains the Registry
C:\Pagefile.sys (or win386.swp) - the default page file
C:\hiberfil.sys - the file to be used during hibernation, i.e. Save System State to Disk
and other windows core components as well as some F-Secure-related files. These files cannot be accessed during scanning as they are protected by the operating system.
Apart from files that are protected by the operating system, applications that are currently running in the background will also not be accessible during the scanning. Minimizing the number of open applications and network connections while performing a scan will minimize the amount of skipped files. Or you can also perform a system scan once your computer starts up before you open any other programs.