A method and apparatus for the measurement of wafer thickness, flatness and the trench depth of any trenches etched thereon using the back surface of the wafer to accurately measure the back side of a trench, rendering the trench an effective bump, capable of being measured on the top surface and the bottom surface through a non-contact optical instrument that simultaneously measures the wavelength of the top surface and bottom surface of the wafer, converting the distance between wavelengths to a thickness measurement, using a light source that renders the material of which the wafer is composed transparent in that wavelength range, i.e., using the near infrared region for measuring the thickness and trench depth measurement of wafers made of silicon, which is opaque in the visible region and transparent in the near infrared region. Thickness and flatness, as well as localized shape, can also be measured using a calibration method that utilizes a pair of optical styli.