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This paper presents the experimental and numerical study of hydrophobic interaction forces at nanometer scale in the scope of engineering micron-sized building blocks for self-assembly in liquid. The hydrophobic force distance relation of carbon, Teflon and dodeca-thiols immersed in degassed and deionized water has been measured by atomic force microscopy. Carbon and dodeca-thiols showed comparable attractive and binding forces in the rage of pN/nm2. Teflon showed the weakest binding and no attractive force. Molecular dynamic simulations were performed to correlate the molecular arrangement of water molecules and the hydrophobic interactions measured by atomic force microscopy. The simulations showed a depletion zone of 2Å followed by a layered region of 8Å in the axis perpendicular to the hydrophobic surface.