Atomic force microscopy (AFM) has been applied to measure inter- or intra-molecular forces acting to hold biological molecules and structures. For these measurements, it is important to keep the target molecules biologically active on a solid surface. Besides the strategy for immobilizing them on the surface keeping their biological activities intact, it is crucial to reduce the force applied to them through the AFM tip to avoid mechanical inactivation of the sample. In this paper, we propose a new procedure to minimize the effect of contact force. The first step of the procedure is to bring the cantilever tip close to the sample surface within less than 3 mum, but short of contact with the sample surface. The approximate distance of the tip from the sample stage is measured using the thermal fluctuation of the cantilever. The second step is a "compression-free" force spectroscopy for the measurement of protein-protein interactions only, which is possible when the piezo scanner was retracted before the cantilever starts upward deflection. The interaction force can be measured in the retraction period provided a physical contact is established between the proteins on the tip and the substrate. This procedure allowed to measure interaction forces between GroEL and a denatured protein without mechanical deformation. (C) 2002 Elsevier Science B.V. All rights reserved.