Creating sub-to few-nanometer defects and nanopores in hexagonal boron nitride (hBN) opens opportunities for engineering quantum emitters and for nanofluidic and sensing applications. Using the electron beam in the aberrationcorrected scanning transmission electron microscope, we demonstrate modification, thinning, and drilling of features in few-layer hBN membranes (∼5 to 20 nm-thick). The atomic composition is monitored with electron energy loss spectroscopy, which also facilitates drift correction. We report effects of electron beam energy and exposure times on defect size and structure. While previous studies focused on beam energies of ≤80 keV to avoid material damage, we show that drilling is favorable at a higher beam energy of 200 keV. The drilling rate at 200 keV is about 10 times larger than at 80 keV (∼1.2 vs 0.1 nm/min), and smaller pores are achievable with minimized damage to the surrounding material. Thinned hBN nanoscale features demonstrate enhanced emission via photoluminescence spectroscopy.