Q. When bookbinding a sefer, sometimes you must drill holes in the pages to repair it. Is the paper dust that comes off the drill bit considered shaymos?
A. Mishna Berura (334: 50) rules that on s'forim that have already been used, the empty margins have the kedusha of the sefer. Rashi (Shabbos 90a) explains that "m'kak" is dust or particles "kol shehu" of s'forim and require geniza or proper dignified disposal in an adequate repository.
There is a biblical prohibition in not following due process (Lo Taasun Ken – Devorim 12: 31, see Mogen Avrohom 154: 9) and Ein Yitzchok Y.D. 1:5 quoting Noda Beyehuda Y.D. 1: 75 that it is only rabbinical).
Daas Kedoshim (282) mentions that only particles that are recognizable require geniza. Ginzei Kodesh (p. 78) further defines these as particles that have some mass to them, as oposed to chalk dust from an erased blackboard or dust from an erased Torah word. (Vedorashto Vechokarto O.H. 72-73)
Horav Shlomo Miller's Shlit'a opinion is that the paper particles created by drilling is considered "m'kak" of Sifrei Kodesh and requires proper geniza. He advised to place a sheet of paper under the sefer prior to the drilling to collect those particles.
Rabbi A. Bartfeld as revised by Horav Shlomo Miller Shlit"a