BleepingComputer.com: Found Hidden Files

I recently downloaded the free version of toolwiz from CNET. It has a function called super explorer that allows you to find and view hijacked or hidden files on your drives. It has shown me several in red.
They are as follows:
A folder named
$Extend
which contains the following files:
$ObjId
$Quota
$Reparse
$UsnJnl
Then there are other files listed under the C: as so:
$AttrDef
$BadClus
$BitMap
$Boot
$LogFile
$Mft
$MftMirr
$Secure
$UpCase
$Volume
If anybody knows what these are and if they are malware, help me figure out how to remove them.

The program you mention...is a self-styled "optimizer". As such, I suggest that you uninstall it and cease to use it or assume that it will do anything of consequence that will be beneficial to your system.

Bleeping Computer DOES NOT recommend the use of registry cleaners/optimizers for several reasons:

• Registry cleaners are extremely powerful applications that can damage the registry by using aggressive cleaning routines and cause your computer to become unbootable.
  
  The Windows registry is a central repository (database) for storing configuration data, user settings and machine-dependent settings, and options for the operating system. It contains information and settings for all hardware, software, users, and preferences. Whenever a user makes changes to settings, file associations, system policies, or installed software, the changes are reflected and stored in this repository. The registry is a crucial component because it is where Windows "remembers" all this information, how it works together, how Windows boots the system and what files it uses when it does. The registry is also a vulnerable subsystem, in that relatively small changes done incorrectly can render the system inoperable. For a more detailed explanation, read Understanding The Registry.
  
  
• Not all registry cleaners are created equal. There are a number of them available but they do not all work entirely the same way. Each vendor uses different criteria as to what constitutes a "bad entry". One cleaner may find entries on your system that will not cause problems when removed, another may not find the same entries, and still another may want to remove entries required for a program to work.
  
  
• Not all registry cleaners create a backup of the registry before making changes. If the changes prevent the system from booting up, then there is no backup available to restore it in order to regain functionality. A backup of the registry is essential BEFORE making any changes to the registry.
  
  
• Improperly removing registry entries can hamper malware disinfection and make the removal process more difficult if your computer becomes infected. For example, removing malware related registry entries before the infection is properly identified can contribute to system instability and even make the malware undetectable to removal tools.
  
  
• The usefulness of cleaning the registry is highly overrated and can be dangerous. In most cases, using a cleaner to remove obsolete, invalid, and erroneous entries does not affect system performance but it can result in "unpredictable results".

Unless you have a particular problem that requires a registry edit to correct it, I would suggest you leave the registry alone. Using registry cleaning tools unnecessarily or incorrectly could lead to disastrous effects on your operating system such as preventing it from ever starting again. For routine use, the benefits to your computer are negligible while the potential risks are great.

• Ed Bott's Webog: Why I don't use registry cleaners
  
• Do I need a Registry Cleaner?

Louis

Those files / folders are hidden for a reason, and they are protected operating system files and folders. They should not be touched. Doing so will cause your computer to not boot or to not function as it should.