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I am planning to do a clean install of Mountain Lion (on a Macbook Pro that was updated to Yosemite) after being told that I have some corruption in my hard drive. The computer (only 3 years old) has slowed down significantly in the last few months, especially when opening directories containing large amounts of files and when loading large documents in Photoshop and other applications. I had doubled my RAM (as a bandaid solution) and that seemed to make a difference for a while, but I now I need to do something about it.

The question is, after I've backed up all of my files onto an external drive with Time Machine and performed the clean install, how do I know what files are safe to copy back into my system? Thanks in advance for the help.

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The short answer is that there is no easy way to know what files have been corrupted and what impact they may have.

The best solution is to rely as little as possible on the files on the old backup. You have made a good start by doing a clean OS install. Now re-install all applications from scratch, preferably by downloading brand new installers. Once you have done that then get all your documents, music and other data files from the backup but not such things as your Library folder. Thi means you will have to set the preferences on all your applications again.

This is a lot of work but the safest way to do a clean install.

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