A method of height measurement based on vibrating mode scanning polarization force microscopy is developed and applied to soft molecules such as dsDNA and antibodies. In the experiment, a bias voltage is applied to a conductive atomic force microscopy (AFM) tip to maintain it farther from the surface during imaging in vibrating mode. By changing amplitude setpoint (A(sp)) the tip can be lowered from the top of a molecule to the substrate, and the displacement of the tip in the z direction (D-Z) approximates the true height of this molecule. This method is first applied to rigid colloidal gold particles and then to dsDNA and antibodies. The measured heights of gold particles are consistent with those in normal tapping mode AFM (TM-AFM). However, the measured heights of dsDNA molecules and antibodies CA125 are much larger than the results in TM-AFM. We deduce that tip pressure might have caused large deformation on soft biomolecules when imaging is performed in ITM-AFM. (C) 2003 American Vacuum Society.