The widespread availability of nanostructures and nanodevices has placed strict requirements on their comprehensive characterization. Herein, in situ techniques are demonstrated to have created a rare opportunity to accurately analyze the intrinsic properties of individual nanostructures and to accomplish the smart design of nanodevices made from these nanostructures. This paper reviews recent developments in in situ fabrication and characterization technologies established within various types of microscopes and the rich information they may provide. The in situ techniques are shown to be important for exploration of many intriguing phenomena at the nanoscale which may then be followed by the smart integration of nanostructures into real functional devices. Successful in situ detection results are presented and discussed, especially in the areas of energy generation, biological imaging and water pumping. Finally, we conclude this article with an examination of the existing challenges and the outlook for this quickly emerging field.