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This paper presents two novel estimation methods that are designed to enhance our ability of observing, positioning, and physically transforming the objects and/or biological structures in micromanipulation tasks. In order to effectively monitor and position the microobjects, an online calibration method with submicron precision via a recursive least square solution is presented. To provide the adequate information to manipulate the biological structures without damaging the cell or tissue during an injection, a nonlinear spring-mass-damper model is introduced and mechanical properties of a zebrafish embryo are obtained. These two methods are validated on a microassembly workstation and the results are evaluated quantitatively.