System files used by Windows are hidden by default to protect these files from accidental deletion or being modified by Windows users. If you noticed that your files or folder are gone, don't panic viruses and spywares often change the attribute of the file or folder to hidden attribute so you won't be seeing them especially if your files are stored on an usb flash drive.
To lunch Folder Options in Windows 8, click on File Explorer. In the File Explorer Windows click on the View Tab and then click on the Options menu and then clicking on the Change folder and search options.
To lunch Folder Options in Windows 7, click on Start menu then clicking on the Control Panel. Change View by: Large icon or Small icon, click on Folder Options to lunch the Folder Options window.
To lunch Folder Options in Windows Xp, click on Start menu then click on My Computer. In the My Computer window, click on Tools menu then click on Folder Options.
To show hidden files, folders and drives in Windows 7, Windows 8 and Windows Xp
To show hidden Files, Folder and drives click on the View tab on the Folder Options, scroll down on the Advancce settings until you see a radio button that says Show hidden files, folders, and drives and then click on it. Also uncheck the Hide protected operating system files (Recommended) to show hidden system files and folders.
After clicking the OK button you should see greyed files and folder on your drive as shown in the image below. A greyed file or folder indicate that it is hidden. Note that some viruses and spywares will disable the showing of hidden files and folder even if the Show hidden files, and folders, and drives is selected and the Hide protected operating system files is unchecked, in this case suspect that your computer might be infected with a virus.