Then you have lost the files. I hope you have some type of backup system installed, if not that is your #1 thing to do. Operating any computer without a backup plan is a 100% guarantee of lost data as you are finding out. Please refer to Back up your Mac with Time Machine, all it requires is an external HD. Many experienced users on these forums prefer the OWC Mercury Elite Pro due to it's high reliability, reasonable pricing, support and when the internal HD dies it is simple to replace.
Also, please remember that Mac OS is extremely stable and operates best if simply left alone. NEVER EVER install third party antivirus, cleaning or other third party maintenance apps, Mac OS simply does not need them and adding them tend to have the opposite effect users want. They make Mac OS slow, appear buggy and do extremely odd things.
Okay, I am off my soapbox now.