The response of host organism in macroscopic, cellular and protein levels to biomaterials is, in most cases, closely associated with the materials' surface properties. In tissue engineering, regenerative medicine and many other biomedical fields, surface engineering of the bio-inert synthetic polymers is often required to introduce bioactive species that can promote cell adhesion, proliferation, viability and enhanced ECM-secretion functions. Up to present, a large number of surface engineering techniques for improving biocompatibility have been well established, the work of which generally contains three main steps: (1) surface modification of the polymeric materials; (2) chemical and physical characterizations; and (3) biocompatibility assessment through cell culture. This review focuses on the principles and practices of surface engineering of biomedical polymers with regards to particular aspects depending on the authors' research background and opinions. The review starts with an introduction of principles in designing polymeric biomaterial surfaces, followed by introduction of surface modification techniques to improve hydrophilicity, to introduce reactive functional groups and to immobilize functional protein molecules. The chemical and physical characterizations of the modified biomaterials are then discussed with emphasis on several important issues such as surface functional group density, functional layer thickness, protein surface density and bioactivity. Three most commonly used surface composition characterization techniques, i.e. ATR-FTIR, XPS, SIMS, are compared in terms of their penetration depth. Ellipsometry, CD, EPR, SPR and QCM's principles and applications in analyzing surface proteins are introduced. Finally discussed are frequently applied methods and their principles to evaluate biocompatibility of biomaterials via cell culture. In this section, current techniques and their developments to measure cell adhesion, proliferation, morphology, viability, migration and gene expression are reviewed.