Q. When we say that lechatchila the Chanuka lights should be lower than ten tefachim is that measure from the flame or from the base of the menora itself? How about for the above three tefachim minimum?

A. Poskim rule that the shiurim or measurements mentioned in regards to a menorah being lower that twenty amos, between ten tefachim or higher than three tefachim from the ground, are all measured from the flame itself and not from where the menorah is standing. (Aruch Hashulchan 671: 22, Kaf Hachaim ibid. 52, Mekor chaim ibid. 6, Nitei Gavriel 16: 7 n. 13)).
Horav Shlomo Miller’s Shlit’a opinion is similar. The Rov also added that when the flame is large, you need to have the complete flame inside the permitted dimension.

Rabbi A. Bartfeld as revised bt Horav Shlomo Miller Shlit’a