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Nanostructured topological insulators (TIs) have the potential to impact a wide array of condensed matter physics topics, ranging from Majorana physics to spintronics. However, the most common TI materials, the Bi$_2$Se$_3$ family, are easily damaged during nanofabrication of devices. In this paper, we show that electron beam lithography performed with a 30 or 50 kV accelerating voltage -- common for nanopatterning in academic facilities -- damages both nonmagnetic TIs and their magnetically-doped counterparts at unacceptable levels. We additionally demonstrate that electron beam lithography with a 10 kV accelerating voltage produces minimal damage detectable through low-temperature electronic transport. Although reduced accelerating voltages present challenges in creating fine features, we show that with careful choice of processing parameters, particularly the resist, 100 nm features are reliably achievable., Comment: 10 pages, 5 figures