The principles, advantages and disadvantages of scanning tunnel microscope (STM), atomic force microscopy (AFM) and scanning near-field optical microscope (SNOM) were introduced and compared. The current applications of STM, AFM and SNOM to imaging and manipulating nanostructure of biomacromolecules, such as polysaccharides, starch, proteins and lipids were focused in food systems. These show that STM, AFM and SNOM provide a basis for examining the macromolecular structure of foods under different conditions, and that they have a great potential prospect in the mapping of structure of food system.