Also, for those using the 3DS as the portable version of their WiiU file, remember that you cannot copy your WiiU data to the 3DS unless the 3DS version of monster hunter is completely data free.
If you already have a file on the 3DS, you will have to purge it. To do this, go to the options menu of MH3U and press and hold L+R+X for 3-5 seconds. This will bring up the data wipe menu, and you can delete all the MH3U save data off your 3DS. Once this is done, you can use the data transfer tool to bring over your WiiU information.
Like DCJ already stated, once you transfer your data back to the WiiU, the 3DS MH3U data will be deleted. Which makes it easier to transfer data back.