This paper focuses on numerical computation and experimental examination of Bernoulli picker, which is the essential module for the 3D stacking process for heterogeneous integration devices, to reveal the fundamental physics of non-contact die handling and to seek optimized design. We estimated the pick-up performance of the Bernoulli picker and the deformation of the die using pseudo-coupling of flow and structural analysis. We simulated the flow field around the target die and picker using the RANS equation with the k-w SST turbulence model to predict the levitation height between the picker surface and target die. Then we estimated the deformation of the die using the inertial relief approach of ABAQUS with computed pressure field information. Based on the numerical investigations, we made a prototype of a Bernoulli picker and conducted experimental measures to verify the feasibility of our design. The measured results indicate that the present numerical approach can be utilized for further optimization.