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Observation of intrinsic quantum transport properties of two-dimensional (2D) topological semimetals can be challenging due to suppression of high mobility caused by extrinsic factors introduced during fabrication. We demonstrate current annealing as a method to substantially improve electronic transport properties of 2D topological semimetal flakes. Contact resistance and resistivity were improved by factors up to 2×106 and 2×104, respectively, in devices based on exfoliated flakes of two topological semimetals, ZrSiSe and BaMnSb2. Using this method, carrier mobility in ZrSiSe was improved by a factor of 3800, resulting in observation of record-high mobility for exfoliated ZrSiSe. Quantum oscillations in annealed ZrSiSe appeared at magnetic fields as low as 5 T, and magnetoresistance increased by a factor of 104. We argue that a thermal process underlies this improvement. Finally, Raman spectroscopy and analysis of quantum oscillations in ZrSiSe indicate that the phonon modes and Fermi surface area are unchanged by current annealing.