I used to open my NTFS File System pendrive on Windows 7. When I opened it on Windows XP, it opened a folder with a autorun file, this autorun file brought me to the content of my drive. The same happened with Windows 8. I thought that deleting that autorun file may allow me to open it directly on all OS. So I deleted that file. Since then, my pendrive shows that its 13gb full(which it already was), but doesn't show anything inside it. I can access files which are not visible by searching on pendrive. The newly copied files are directly accessible. I have also set the Show hidden files to true in Folder options. I neither remember names of all files and folders on the drive so that I can search and backup files, nor want to lose the files by Formatting.
Finally, I found a solution on my own. I was in Folder Options. I unchecked 'Hide protected operating system files', tried, and found a new unnamed folder. I opened it, and all my files were there.