In certain types of biomimetic surgery systems, micro robots inspired by Paramecium are designed to swim in a capillary tube for gaining access to internal organs with minimal invasion. Gaining insights into the mechanics of Paramecium swimming in a capillary tube is vital for optimizing the design of such systems. There are two approaches to modeling the physics of micro swimming. In the envelope approach which is widely accepted by researchers, Paramecium is approximated as a sphere self-propelled by tangential and normal surface distortions. Not only this approach is incapable of considering the specific geometry of Paramecium, but also it neglects short range hydrodynamic interactions due to beating cilia. Thus it leads to dissimilarity between experimental data and simulation results. In this study, it is aimed to present a sub layer approach to modeling Paramecium locomotion which is capable of directly applying the hydrodynamic interactions due to beating cilia on Paramecium boundary. In this approach, Paramecium’s boundary is discretized to hydrodynamically independent elements; in each time step of swimming, a specific function is fit to Paramecium boundary. Then, element coordinates are extracted and fluid dynamic equations are solved to model the physics of micro swimming.