Though tissue mechanics serve an important biological function, as in embryonic organ development, a paucity of experimental methods exists to measure these interactions. We used an atomic force microscope (AFM) to measure local mechanical properties of unfixed cryosections of mouse embryonic tooth, which served as a model for organ morphogenesis. AFM is commonly used for tissue indentation; however, most of these studies analyze adult tissues that are mechanically more robust than embryonic tissues, and thus existing experimental protocols do not address the technological limitations of AFM indentation into extremely soft materials ( 50%) between the software-prescribed and actual applied loads that arise from tissue deformation and the artifacts just mentioned. Since there is no closed-form solution to the integral of the noisy load history, analysis of the indentation data is more complicated. To address this, we took a numerical approach, which produced an average correction of 11% in the instantaneous shear modulus, 10% in the infinite-time shear modulus and 19% in the creep function time constant of relaxation in data from 20 indentations. In addition, this approach was able to successfully resolve subtle differences (<10 Pa) in local tissue stiffness. Thus, our method produces a more sensitive and accurate viscoelastic measurement of extremely soft embryonic tissues, which may greatly aid in uncovering the micromechanical determinants of embryonic tissue development.