Jesus was referring to their custom of bathing in the nearest stream and then walking home on a dusty road. The physical body was still clean except for the feet, The rich of that day kept jars of water inside the home that were used only by the servants to wash the master’s feet after the walk home. That is why Jesus said, you are clean except for your feet and you need only to wash them to be totally clean on the outside. But, as usual, I believe that Jesus was using a well-known custom to convey a deeper message. Notice that Jesus said, “”And you men are clean, but not all of you” referring to Judas who He knew would turn against Him and betray Him to the religious leaders. I believe that Jesus was telling the disciples that once they were washed by the blood of Jesus that they were completely clean on the inside. Since we still have to live in the flesh in this world, there are times that we will need to come back to the stream of living waters, not to be saved again, but to repent of the times we fail and come up short of the mark.
8 If we say that we have no sin, we deceive ourselves, and the truth is not in us.
9 If we confess our sins, he is faithful and just to forgive us our sins, and to cleanse us from all unrighteousness.–1 John 1:8,9 (NCV)
Even though Judas was with Jesus and the disciples, it does not appear that he ever accepted Jesus as the Messiah since Jesus said that “not all of you are clean”.