Techniques are disclosed for stabilizing soft specimen traditionally considered too fragile for APT instruments. These specimens include biological samples, polymers and other fragile materials. For this purpose, a protective structure is disclosed that surrounds the sides of the specimen by supporting walls while only exposing the very end or terminus of the specimen to the electrostatic field of the APT instrument. The protective structure may take the form of a nanoscale conical grinder which continually machines the specimen to regenerate the terminus of the specimen in-situ. Alternately, the protective structure may take the form of a nanopipette in which the specimen is first frozen before undergoing field evaporation together with the tip of the nanopipette. Heretofore only routinely possible for rigid and hard materials, the design thus extends APT analysis to produce three-dimensional atomic-scale maps of soft specimens.