Currently Being ModeratedJan 2, 2013 7:33 PM (in response to rachina)
I have the app Readdle Docs. It allows you to move PDF files to your device and to move them around on your device. Might check it out. ( I think there's an iPad version of the app, but I have the iPhone version and it works, just not as pretty)
THere's also Goodreader, but I don't have experience with it to know if it has folder abilities.