An approach for automated nanotomography, a layer-by-layer imaging technique based on scanning probe microscopy (SPM), is presented. Stepwise etching and imaging is done in situ in a liquid cell of an SPM. The flow of etching and rinsing solutions after each etching step is controlled with solenoid valves which allow for an automated measuring protocol. The thermal drift and the drift of the piezo scanner is corrected by applying offsets calculated from the cross correlation coefficients between successive images. As an example, we have imaged human bone with approximately 10 nm resolution using tapping mode SPM and successive etching with hydrochloric acid.