There are two methods that u can follow.
1) You have to use two microcontrollers 1 for read and another one for write in two different pendrives. The read data is transfered to another pendrive using serial communication TXD,RXD.
2) Another method is you can use a RAM. This method is usedfull in bulk data transfer. It is very fast. For this we have to use DMA concept. Once pendrive is connected read data first wait until it completes reading, then write on another one.