We have patterned sub-1 nm dangling-bond (DB) lines on a H-terminated Si(100)-2 × 1 surface aligned with atomic precision at room temperature using a scanning tunneling microscope (STM) to controllably desorb hydrogen atoms from a H:Si(100) surface. In order to achieve continuous and aligned DB lines, we have performed a detailed investigation of the effects of patterning parameters such as the writing voltage, writing current and electron dosage, as well as STM tip apex geometry on the fabrication and alignment of Si DB lines. We show that there exists an optimum set of patterning parameters which enables us to obtain near-perfect Si DB lines and align them with near atomic precision in a highly controllable manner. In addition, our results indicate that the pattern quality is weakly dependent on the STM tip apex quality when the patterning parameters are within the optimum parameter space.