Protein adsorption on surfaces (microfluidic and microarray devices) is a ubiquitous and complex phenomenon that is governed by the balance of transport of the protein species to the surface (convection, diffusion etc.) and adsorption/desorption at the surface. The extent of binding depends on a variety of factors such as the affinity of the protein to that particular surface, the availability of binding sites, localized concentration of protein in the near wall region and the flow characteristics of the species in that region. Factors such as time varying flows or complex device geometries, the presence of multiple species that compete for the same binding sites, or the possible denaturing of proteins when they attach to the surface make it extremely difficult to quantitatively analyze protein interactions with surfaces. In this work, we have developed and demonstrated a model that evaluates protein adsorption that accounts for both the fluidic transport as well as the biochemical kinetics in complex biomicrofluidic devices. The model is valid under both kinetic (transient) as well as static conditions. An automated procedure was also developed to extract the "intrinsic" or mass-transport independent adsorption kinetic rate constants from experimental data using a least-squares minimization method (variant of Gauss-Newton). The automated, data extraction methodology is applied to two different proteins Alkaline Phosphatase (AP) and Glucose Oxidase that have been brought into contact with PEEK and Teflon capillaries.