Apparatus and method for synthesizing nanostructures in a controlled process. An embodiment of the apparatus comprises a stage or substrate holder that is heated, e.g., resistively, and is the primary source of heating for the substrate for nanostructure synthesis. The substrate and substrate heater are enclosed in a chamber, e.g., a metal chamber, which is ordinarily at a lower temperature than are the substrate and substrate heater during synthesis. Some embodiments of the invention are particularly useful for chemical vapor deposition (CVD), low pressure CVD (LPCVD), metal organic CVD (MOCVD), and general vapor deposition techniques. Some embodiments of the present invention allow for in situ characterization and treatment of the substrate and nanostructures.