What is the way to clean kneaded eraser?
I can see black patches on it. 


That is a part of normal use. Those black marks are graphite, charcoal and etc. that the eraser picked up from your working surface. That is the eraser doing its job as intended.

What you are supposed to do is fold / knead away those "dirty" parts back into the eraser so that non-black (the erasers original colour) parts are exposed so that you don't get unwanted or inefficient transfer. From rapidfireart.com on How to Clean a Kneaded Eraser:


  Because kneaded erasers absorb graphite, they will become dirtier with use. To clean a kneaded eraser, you can stretch and knead it until the color turns light grey. Eventually they will become too dirty to use as graphite, charcoal, dust or other particles accumulate in the eraser.


So, at some point, you won't be able to keep using it and then it will be time to seek a replacement.