In this study, we surveyed the possibility of nanometer scale lithography in ambient condition using a scanning tunneling microscope. Optimized parameters for this purpose have been determined. The study will be hopefully an initiative step toward further progress in manufacturing nano-bio chips and nano-bio electromechanical systems utilized for diagnosis and treatment purposes in medical areas. Tests showed that the scanning tunneling microscope lithography yielded the same result in each test and thus it was reproducible. Using STM microscopy, nanostructures were first created in the form of protruding points on the surface. Then we created linear structures, more complex forms, and finally we were able to write some words. Nanostructures were created on gold surfaces by tungsten, gold, platinum-palladium tips. It is found that the voltage used in lithography is effective on creating nanostructures, and also on the size of nanostructures, so that with increasing voltage, the size of nanostructures increases too. The speed of tip is also another important factor that can affect nanostructures size and their continuity. Time interval between consecutive pulses influences on the nanostructures integration and its value should be specified based on conditions and purposes of lithography. The size of nanostructures ranged between 20 and 150 nm. Tip geometry, humidity and temperature are also likely to be influential factors that require further studies to investigate their effects.