Binnig et al. invented atomic force microscope (AFM) in 1986. It is a scanning tool for nanostructure investigations. It is now consider to be one of the landmarks of modern sciences, with citations of the first article increasing by more than 13,500 times (Binnig et al, Phys Rev Lett 56(9):930, 1986). The AFM has come up as a new addition to macroscopic and microscopic techniques since it has benefits in sample preparation and the ability of high-resolution imaging in both liquid and air environment if compare to standard light microscopy techniques. This sophisticated instrument has successfully been used in all branches of science such as material science ((a) Bhushan et al, J Phys Condens Matter 20(36), 365207, 2008; (b) Johnson, Rubber Chem Technol 81(3):359–383, 2008; (c) Withers, Aston, Adv Colloid Interf Sci 120(1):57–67, 2006), food science (Yang et al, J Food Sci 72(4):R65–R75, 2007), nanofabrication ((a) Simeone et al, J Phys Chem C 113(44):18987–18994, 2009; (b) Tseng et al, J Nanosci Nanotechnol 8(5):2167–2186, 2008), and microbiology for nearly two decades after its invention ((a) Cohen, Bitler, Curr Opin Colloid Interface Sci 13(5):316–325, 2008; (b) Dufrêne, Curr Opin Microbiol 6(3):317–323, 2003; (c) Müller et al, Curr Opin Biotechnol 20(1), 4–13, 2009). The microbiology field has been revolutionized by AFM. It has enriched the realm of sample preparation and microbial surface analysis in particular during the last two decades (Dufrêne, J Bacteriol 186(11):3283–3285, 2004).