We employed atomic force microscopy (AFM) with bias control to fabricate oxided nanopatterns on silicon surface with feature size down to 50nm. The relationship of silicon dioxide nanopatterns against humidity was studied and then the optimal parameter was used to make oxide nanoarry for interaction of biotin and streptavidin. The scanning function of AFM was utilized to verify the different height of biomolecules. According to our experimental results, using nano biochip of silicon dioxide can decrease the monitoring scale to nanometer and can be the nano-platform for monitoring the behavior of biomolecular interaction. We anticipate mimicking the correlation of single molecular behavior and an array of biomolecular behavior to understand the coincidence of them.