Stellar model atmospheres are a fundamental tool for our understanding of stars. Because the chemical composition of stars cannot be measured directly, the inferred stellar parameters are model dependent. In recent years great progress has been made in the modeling of stellar atmospheres, allowing the relaxation of simplifying assumptions made in previous models. The use of new 3D model atmospheres to infer the solar chemical composition has resulted in a decrease of the solar metallicity. This result has caused some controversy and is being challenged. The main aim of this thesis is to ascertain if the new models of stellar atmospheres are realistic and can be trusted to derive the chemical composition of stars in general, and the Sun in particular. Other objectives also include the study of line formation in the Sun at high spatial resolution, and possible implications in the modeling. ...