Commentary for Yadayim 3:4

שמלמעלן ושמלמטן (the upper and lower margins) - that he (i.e., the Scribe) needs to leave free without writing above from the column [in the parchment] three fingerbreadths and one handbreadth below.

The margin on a scroll which is above or below or at the beginning or at the end defiles the hands. Although there is nothing written in the margins of the Tanakh scrolls, they still defile the hands because they are part of the scroll.

שבתחילה ושבסוף – at the beginning of the Scroll he needs to leave free in order to roll all of the Scroll, meaning to say, like the measurement of the circumference of the entire Scroll, that the Scroll, when t is rolled from its end to its beginning is similar to a Mezuzah when they fold it from [the word] אחד/[“God is] one,” directed towards the שמע/[first word of the] Shema. And at its conclusion in order to roll up the scroll of the Law around a cylinder (i.e., a handle). And especially when he doesn’t have anything there other than the Torah alone, he needs to do this, but when he fastens the [text of the] Torah, [the text of] the Prophets and [the text of] the Writings together, he needs to roll up the all of the Scroll at its end, in order to roll the cylinder at its beginning. But if he rolls it towards its beginning, it is found that the Torah (i.e., Five Books of Moses) is from the outside, and it is disgraceful that that Torah should be made into a guardian for the Prophets and the Writings. And it is this that we are speaking f in the first chapter of Bava Batra [13b-14a] and he makes it in order to roll [enough blank parchment wrapped around a cylinder from its beginning and in order that there be a circumference of the Scroll at its end.

Rabbi Judah says: the margin at the end does not render unclean [the hands] until a handle is fastened to it. Rabbi Judah says that the margin at the end of the scroll doesn't defile because it could always be cut off. It only defiles once they have used that extra piece of scroll to attach a handle. Once a handle has been attached the end margin has become a necessary part of the scroll and it too defiles.