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We study the fundamental properties of femtosecond-laser (fs-laser) hyperdoping by developing techniques to control the surface morphology following laser irradiation. By decoupling the formation of surface roughness from the doping process, we study the structural and electronic properties of fs-laser doped silicon. These experiments are a necessary step toward developing predictive models of the doping process. We use a single fs-laser pulse to dope silicon with sulfur, enabling quantitative secondary ion mass spectrometry, transmission electron microscopy, and Hall effect measurements. These measurements indicate that at laser fluences at or above 4 kJ m-2, a single laser pulse yields a sulfur dose >(3 ± 1) × 1013 cm-2 and results in a 45-nm thick amorphous surface layer. Based on these results, we demonstrate a method for hyperdoping large areas of silicon without producing the surface roughness.