Non-invasive manipulation and analysis of biological objects with high resolution and efficiency have become extremely important. This dissertation presents three novel techniques based on light scattering and optical forces, which could bring high resolution and speed to submicron cell characterization, improve the throughput and functionality of self-propelled cell analysis and enhance the parallelism, portability and flexibility of cell manipulation instruments. Elastic light scattering is used for submicron cell characterization. An important problem in oceanic microbial ecology is characterizing the constituents of the sea. To pursue this goal, the application of angularly-dependent light scattering on oceanic microbe differentiation has been explored. Good overall agreement is found between scattering patterns simulated with developed models and those experimentally measured. The distinct scattering patterns of different species provide fingerprint information that will allow for routine identification of marine picoplankton. Optical tweezers have been used not only for manipulating cells, viruses and organelles within cells, but also measuring biological forces on the order of picoNewtons. In the second part of this dissertation, a three-dimensional resizable annular laser trap is developed for self- propelled cell manipulation and analysis. This system offers high power efficiency and is potentially useful for high-throughput multi-level sperm sorting based on motility and chemotaxis. With only tens of milliwatts devoted to each sperm, this new type of laser trap offers a gentle way to study the effect of optical force, laser radiation and external obstacles on sperm swimming patterns and membrane potential in detail. Applications could be extended to motility and biotropism studies on other self-propelled cells, such as algae and bacteria, etc. The third part of this dissertation involves manipulation of multiple biological cells both synchronously and independently. Substituting Vertical Cavity Surface Emitting Lasers (VCSELs) for standard diode and gas lasers in optical micromanipulation provides the ability to meet the miniaturization and parallelism demands of current lab-on-a-chip technologies, so that multiple experiments can be performed in parallel and at low costs. By combining a single VCSEL trap that can move individual particles in 3-D with a VCSEL trap array, a micromanipulator capable of multi-step group operating and cell rotating is constructed