In order to use an atomic force microscope to measure the intramolecular mechanics of a single protein or polymer molecule. the very initial stage of stretching must be recorded without complications from nonspecific adhesions of target molecules to substrate materials. Although polyethylene glycol itself shows a certain level of adhesion to the functionalized surface of crystalline silicon wafer used as a substrate, adhesion of polypeptides and proteins can be minimized by covering the substrate surface with flexible polyethylene glycol chains. Determination of the cantilever spring constant is also important ill the quantitative analysis of the result of force measurements. We introduce a hydrodynamic method of cantilever calibration as an effective method of estimating the relative spring constant of the cantilever. Finally, for mechanical manipulation of DNA, we introduce the use of a positively charged glass surface to keep DNA molecules in the stretched conformation for molecular manipulation including mechanical cutting of stretched DNA. (C) 2002 Elsevier Science B.V. All rights reserved.