The atmospheres of chemically peculiar stars can be highly structured in both the horizontal and vertical dimensions. While most prevalent in the magnetic stars, these structures can also exist in non-magnetic stars. In addition to providing an important window to understanding the physical processes at play in these complex atmospheres, they can also be exploited to study stellar pulsations. This article reviews contributions to the session “A 3D look into the atmosphere” of the Joint Discussion “Progress in understanding the physics of Ap and related stars”. It is divided into 3 sections: “Magnetic field and surface structures”, “Pulsations in the atmospheres of roAp stars/inversions”, and “Spectral synthesis/atmospheric models”.