A method for measuring nm-scale tip-sample capacitance including (a) measuring a cantilever deflection and a change in probe-sample capacitance relative to a reference level as a function of a probe assembly height; (b) fitting out-of-contact data to a function; (c) subtracting the function from capacitance data to get a residual capacitance as a function of the probe assembly height; and (d) determining the residual capacitance at a z-position where the cantilever deflection is zero.