This paper presents fluid modeling and simulation of microchambers within microfluidic chip for immunoassay based biosensing applications. A microfluidic biosensor chip for fluorescence based immunoassay detection of biological elements should include suitably designed chambers with rinsing channels. Microfluidic chambers are necessary in holding and immobilizing enzymes onto the microfluidic surface. They function as center of interest for enzyme interactions and optical detection. It is also necessary to incorporate cleaning function into the micro-chambers to instigate reusability. The shape and size of the chamber is a crucial factor for sensitivity of the integrated biosensor as the optical detection unit would be placed at the top of the chamber. In the present work, combinations of chambers and channels with various geometries and sizes are simulated for rinsing flows. Chambers are analyzed for rinsing behavior under certain pressure drops between the inlet and outlet channels. Average velocity and flow contours are plotted and compared at different cross-sections within the chambers. Simulations are performed using FEM software, FEMLAB (Comsol, Inc., Burlington, MA). Optimized chambers are selected based on optimal rinsing, negligible slow zones without reverse flows, relatively simple geometry and low pressure drops.