Thanks modey3 for your detailed answers,
But I think although Secondary Electrons (SE) are knocked out of the wafer surface, there are great amount of "new" electrons emitting from the gun impinge on the wafer that will compensate the loss of SE's. So there are two situations:
a) SE Yield <1, means there are excessive electrons on the wafer, thus negatively charged wafer surface is achieved ? ( suppose no/few electrons go through the silicon)
b) SE Yield>1, More SE's are generated and then grounded as you said, hence it's possible to have a positive surface filled with holes. And an external positive voltage/efield will prevent the positive holes from going deeper into the wafer, namely they are likely to be kept on the wafer surface...
xlee790