The atmosphere of the Sun is highly structured and dynamic in nature. From the photosphere and chromosphere into the transition region and the corona plasma- β changes from above to below one, i.e., while in the lower atmosphere the energy density of the plasma dominates, in the upper atmosphere the magnetic field plays the governing role - one might speak of a "magnetic transition". Therefore the dynamics of the overshooting convection in the photosphere, the granulation, is shuffling the magnetic field around in the photosphere. This leads not only to a (re-)structuring of the magnetic field in the upper atmosphere, but induces also the dynamic reaction of the coronal plasma, e.g., due to reconnection events. Therefore the (complex) structure and the interaction of various magnetic patches is crucial to understand the structure, dynamics and heating of coronal plasma as well as its acceleration into the solar wind. The present article will emphasize the need for three-dimensional modeling accounting for the complexity of the solar atmosphere to understand these processes. Some advances on 3D modeling of the upper solar atmosphere in magnetically closed as well as open regions will be presented together with diagnostic tools to compare these models to observations. This highlights the recent success of these models which in many respects closely match the observations.