I am wondering is it is possible to clone a cf with a qnx file system using a usb cf to usb adapter? will there be any problem if i try to copy using usb?
Yes, should be possible, if you can open the CF card in WinHex as a physical medium (Tools | Open Disk).
If you have two USB card readers, the card could be cloned directly. Otherwise you create an image file of the card and then restore that image file back to the target card.