I am currently writing my undergraduate final year thesis. It happens so that I have to consult papers written by my thesis examiner on a particular topic. My question is is it appropriate to seek clarification from him on parts which I'm unsure of in his paper even though he is my examiner? I tried asking my supervisor first but he is unsure about it as well as this is not within his area of expertise. (I need some results from other branches to prove something.)
This is perfectly acceptable.
Caveats: I would be wary about asking questions you should know the answer to. I would also avoid anything that might be interpreted as a criticism. I know this sounds obvious but its an easy mistake to make. If you are not a tiny bit careful, "Please clarify X" can easily be read as "X wasn't clear".
If your advisor isn't clear you're covered that it's not a 'trivial' or stupid question.
If you are careful about how you word the question, you shouldn't be in any danger of offending anyone. Explaining things can be tricky and if you are outside the immediate field, it doesn't look bad for anyone that you didn't follow.
Conversely not asking could end up reflecting badly on you. He will in all likelihood: understand the issue, see how it applies to your situation, and will be interested in your response/use of his results. If you don't follow it will probably be clear. If on top of that you missed (what he will see as) an easy step to rectify the situation - ask, exactly as you suggest - he may well see it in a negative light.
Finally if for some nuanced reason - and I really can't think what this would be - there was a reason he wouldn't be happy to discuss this with you: if you ask in a way that doesn't demand or expect an answer no harm will have been done.