The microelectronics industry has long sought an aqueous etchant that could produce atomically flat Si(100) surfaces by anisotropic etching. This dissertation shows that near-atomically-flat Si(100) surfaces can be produced by an aqueous silicon etchant - 40% NH4F (aq.). The etching of Si(100) in 40% NH4F (aq.) produced H2 bubbles as a reaction product, which led to significant roughening of the surface if not removed. A near-atomically flat surface was produced if the bubbles were periodically removed from the etching surface. Analysis of the infrared spectrum of the NH4F-etched surface showed that the surface was H-terminated. A new spectral deconvolution technique led to reinterpretation of the spectral bands and revealed the surface structure that is consistent with the STM images of the surface. Investigations of the bubble-induced roughening of Si(100) surface during NH4F etching revealed a new mechanism of {111} microfacet formation on this surface. To understand the etch kinetics that produced the observed morphologies, a fully atomistic kinetic Monte Carlo simulation of Si(100) etching was developed. The simulations showed that previously postulated models of H/Si(100) etching based solely on bond counting or interadsorbate stress cannot explain the experimental etch morphologies. The simulations suggested mechanisms that lead to the formation of flat stripes, hillocks, and rough morphologies observed on etched Si(100) surfaces. The production of long rows observed on the NH4F-etched Si(100) surface could only be explained by the fast etching of dihydrides bonded to monohydrides - termed as "[alpha]-dihydrides". In addition, a comprehensive study of the vibrational spectrum of various Hterminated Si surfaces produced by NH4F (aq.) etching was performed using density functional theory. The simulations predicted stretch mode energies within 2% of the experimentally observed; however, the accuracy of the calculations was strongly affected by interadsorbate strain. Simulation of point defects on H/Si(100) surfaces provided insights into the origin of large heterogeneous broadening observed on NH4F-etched Si(100) surfaces.