Clean,
as it is used in these verses, means,

Clean, clear, pure, fair.
Also,
Free from guilt, morally innocent.

Or,

To cleanse, 
purge, purify.  
  Now ye are clean through the word which I have spoken unto you. 
Abide
in me, and I in you. 
As the branch cannot bear fruit of itself, except it abide in the vine;
no more can ye
except ye abide in Me

John 15:3-4
     
And there came a leper to Him, beseeching Him, and saying
unto Him, If thou wilt,
thou canst make me clean.
And Jesus, moved with compassion, put forth His hand, and touched Him, and saith unto him,
I will; be thou clean.

  Mark 1:   
40-41