Good topic. I agree with the others--stir well, obtain a few drops with your pipette, place a few drops on your room temp refractometer and put the cover on right away. Random particles don't matter.
My first plastic pipette was put away after a nice brewday with several refractometer readings and any extra "samples" going right into my mouth. When I opened up the case for the next brewday, the pipette was all moldy. Needless to say, I tossed the pipette in the garbage.
To prevent a recurrence, all subsequent pipettes have been quickly rinsed with water and sanitized with StarSan before being put away at the end of the brew day. No need to keep replacing plastic pipettes, unless you lose them.
If you really want to know more about the refractometer, we had a good discussion about this earlier this year.http://www.homebrewersassociation.org/forum/index.php?topic=2307.45