Hello masoomsahib and welcome to Seven Forums.
If "some other program" deleted your prefetch folder, I'd be concerned about malware on your computer. Even deleting the contents
of the prefetch folder can affect computer performance. The prefetch folder is a subfolder of the Windows system folder. Does Deleting the contents of a "PREFETCH" folder affect the - Microsoft Answers
I'd start out by scanning your computer for malware with whatever antivirus and antispyware you have installed. Make sure it's updated and run a full scan, not a quick scan. Then I'd run some additional on-demand scanners to double check your system. (No antimalware program is 100% effective 100% of the time. If there was such a thing we'd all be using it.) These scanners are usually recommended and they all have free versions: Malwarebytes
| Hitman Pro
. There are several others available but these should help. Again, make sure they're updated and run full scans.
If your machine comes back clean I'd next try running a System File Checker scan from an elevated command prompt (option two, this tutorial.) The scan looks for and tries to fix damaged or corrupt system files. If problems are found run the scan 3 times rebooting in between each scan. SFC /SCANNOW Command - System File Checker
And one other thought. Windows 7 doesn't need tweaking by third party "tuneup" tools. Those tools can do more harm than good. If anyone insists on using them they need to know exactly what the tool is doing to the system so they can reverse any damage done. At a minimum I suggest making a restore point before running a tuneup tool. Better yet, a full system image.
Please post back with your results.