We describe various techniques to manipulate laser-cooled Ne atoms interferometrically by using a silicon nitride film with holes and electrode deposition. Laser-cooled Ne atoms pass through a computer-generated through-hole binary hologram and generate an atomic image on a substrate. The hologram can be designed to provide a spherical phase correction, and the reconstructed pattern is focused on the substrate at a finite distance from the hologram. Such holographic manipulation can be extended to gray-scaled reconstruction that is used to deposit relief-like 3D atomic patterns on surfaces. In addition, an atom interacts with electric, magnetic, and optical fields. This provides the holographic atomic-wave manipulation to perform functions that are difficult for a light wave. The Stark shift induced by an external electric field is used to switch and to modify atomic patterns in real time. We also introduce an reflecting type atom holography by using quantum reflection.