We present a novel technique which allows for the investigation of block copolymer microstructures on various substrates and at different depths. Using a low voltage, high resolution scanning electron microscope (SEM), we examined the topography and underlying morphology of poly(styrene)-poly(butadiene) diblock copolymer films. The internal morphology of the film was exposed for SEM imaging by using a non-selective fluorine-based reactive ion etching (RIE) technique. By controlling the depth of the RIE etch we removed the surface layer of poly(butadiene) and exposed the microphase separated structure underneath for SEM imaging. After obtaining SEM images of this exposed layer, we subsequently removed this layer with further RIE to obtain SEM images of the layer underneath. By continuing this procedure, we can obtain images of the microstructures as a function of depth with a 4-nm lateral resolution and a 10-nm depth resolution.