In the semiconductor industry you'd be using plasma etching.

If I understand the situation correctly, you begin to see build up after several uses.  In water, and even the borate buffer, the PEI is sufficiently basic to become protonated and form a polycation.  On one hand you want this - the polycationic coating helps your cells (which have anionic head groups on the lipid bilayer) to stick to the surface.  But it creates problems since it can form aggregates with anionic substances - such as any cells that are partially lysed and leave fragments of the anionic membrane, or the anionic detergent (tergazyme).  These polyplexes are fairly insoluble.  You can use pH to dissolve them - but it takes a pretty high pH to deprotonate the PEI or pretty low pH to protonate the anions.  If your MEA surface can take it, something that oxidizes the organics might work - hydrogen peroxide or ozone or some such. (Clorox 2 is hydrogen peroxide and detergent).  Nochromix is a good oxidizer - but is very acidic.  These kinds of films are hard to remove - the enzymatic detergent is good on protein residues, but not so much on synthetic PEI. 

Hi Carolina Maciel Camargo, Greetings ... PEI could be dissolved by using either Methylene Chloride or Tetra-hydro Furan. I am not sure if these solvents may be used from Environmental rules angle. But, they are good for the task here - I feel so

In the semiconductor industry you'd be using plasma etching.

agreed with Alan F Rawle with carefully controlled plasma etching you can remove these coatings. 

Thank you all for your help! James, I really appreciate your detailed explanation behind the chemistry of what is going on, thank you! I have tried several acids and it does help, but unfortunately it also destroys the electrodes... I haven't tried the hydrogen peroxide, and I like the Clorox idea since it also contains the detergent. I'll try that! Hariharan, I have never used these solvents. I will check to see if we can use them on our MEAs! Alan and Muzammil, plasma cleaning definitely helps! However, when the surfaces have already accumulated a lot of PEI, it doesn't remove most of it. But that could be because the plasma cleaning hasn't been applied long enough in order to remove it all (since it could then damage the electrodes). Thank you all for your very helpful suggestions!

hi Carolina Maciel Camargo, my experience with PEI was based on a method that I had used to develop a Molding method that molds PEI (a high melting Polymer) at Room temperature. The Solvent Casting method was used. Thus, my expression about the possibility of "removing" PEI from surfaces under consideration is based on that real work. Best wihses