In the "White Room" episode. Nasedo says that he can't get past the security scanners because they use X-rays and his bone structure is not human. Then at the end of "Destiny" they decide that he will shape-shift into Agent Pierce and take over the special FBI unit that has been hunting them. They never explain, however, how he will be able to function as a phony Pierce when he still can't get past the X-ray scanners.