USB/flash memory malwares depend on the "autorun.inf" file to spread.
When you plug a USB into your computer, the AutoRun feature starts and an .exe file is started from it and infect your computer. After that, it infects all the mounted drives with the same method. Put a copy of itself in the root of all drives, along with autorun.inf file. Then, they disable "Show hidden files" from Folder Options, by editing the registry. Maybe also auto close, or disable, the Task Manager to prevent you from killing its process.
Even if you removed the infected file from the USB, and reformatted your C: drive and installed a clean version of Windows, it is still hiding in your other drives (D:, E:, etc.) and as soon as you open any of these drives after a clean install of Windows, you will get infected again.
Cleaning your computer while the malware is active is a bit tricky. If you removed the .exe+autorun.inf from an infected drive, then it copies itself again to the same drive. If you killed its proccess, it waits till you open one of the infected drives, and it starts again.
A quick fix for this kind of malware is to disable the AutoRun feature and/or install an application like Autorun Eater that will monitor, scan, and allow/deny autorun.inf when one is detected. Also, it lets you fix the Folder Options and Task Manger settings in the registry if they were being modified, and restore them to their original state.
1First get rid of that malware that infected your PC. The issue you describe is a symptom that something bad is happening, and not seeing hidden files is probably not the only problem you will be confronted with. – jaume – 2013-03-09T19:29:49.567
1How do I get rid of malicious spyware, malware, viruses or rootkits from my PC? – Ƭᴇcʜιᴇ007 – 2013-03-09T19:34:20.017
I used this http://download.cnet.com/Malwarebytes-Anti-Malware/3000-8022_4-10804572.html?tag=mncol%3B6
– Faeze – 2013-03-10T20:26:00.097I used this link: http://download.cnet.com/Malwarebytes-Anti-Malware/3000-8022_4-10804572.html?tag=mncol%3B6. And also I scanned my flash memory with KasperSky.
– Faeze – 2013-03-10T20:27:22.887