The best thing about MSE is that it's very lightweight on computer resources as well, but it's got a very high detection rate.
System File Checker is an executable in your Windows directories that is used through command prompt. It parses command line arguments into specific instructions that tell it what you want to scan and what it repairs.
To use it:
1) Start menu, type in "Run" (without quotes) and hit enter to open the Run command
2) Type "cmd" (without quotes) and hit enter
3) In command prompt type in the following command:
It will take some time, but once it's done it will output the results to CBS.log and notify you whether it's actions were successful or not and whether it needed to take action based on the file integrity check.