AbstractScanning probe microscopies, such as scanning tunneling microscopy and atomic force microscopy, are uniquely powerful tools for probing the microscopic properties of surfaces. If these microscopies are used to study low‐dimensional materials, from two‐dimensional solids such as graphite to zero‐dimensional nanostructures, it is possible to elucidate atomic‐scale structural and electronic properties characteristic of the bulk of a material and not simply the surface. By combining such measurements with chemical synthesis or direct manipulation it is further possible to elucidate relationships between composition, structure, and physical properties, thus promoting an understanding of the chemical basis of material properties. This article illustrates that the combination of scanning probe microscopies and chemical synthesis has advanced our understanding of charge density waves, high‐temperature superconductivity, and nanofabrication in low‐dimensional materials. This new approach to studying materials has directly contributed to our knowledge of how metal dopants interact with charge density waves and elucidated the local crystal chemistry of complex copper oxides, microscopic details of the superconducting states in materials with a high superconducting transition Ic, and new approaches to the fabrication of multi‐component nanostructures. Coupling scanning probe microscopy measurement and manipulation with chemical synthesis should provide an approach to understanding material properties and creating complex nanostructures in general.