If you are trying to figure out whether all the files on your Windows system partition are correct and unmodified, and there are no hidden files added by viruses, rootkits or malware, you may find it a challenge to complete your task. If you have no ideas on how to do, just check out the methods given below.
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1, Using disk imaging software
There are many excellent disk imaging freeware as well as commercial software, such as Acronis True Image and DriveImage XML, they provide you the ability to create an image of the entire system partition, when your system is clean, you can use these utilities to make an entire system backup, you can then revert your system to a former clean state in a few minutes at any time.
2, Using folder monitor program
There tools could monitor files activities on the windows system for you, when a file is created, changed or deleted, you will be notified and the event will be logged.
3, Using MD5 generator
MD5 is a commonly used cryptographic hash function to check the integrity of files and folders. If two files have the same MD5 checksum, they are believed to be identical.
You can create a snapshot of your system by generating and saving the MD5 hash value of all the files on your system partition, when you want to check the integrity of them, just boot up your computer with a live cd like Windows pe cd, then compute the md5 checksum of all files, and compare the result with the one you saved before.