Microscale total analysis systems have promising characteristics for small scale high throughput, multiplex analysis. This research involves developing unit operation systems using a three-dimensional hybrid microfluidic/nanofluidic system made of poly(methylmethacrylate) and poly(carbobate), which is a form of a microscale total analysis system developed in our group. The generic form of one unit operation system is composed of two spatially separated microfludic channel layers interconnected by a nanocapillary array membrane (NCAM). The nanofludic component (NCAM) adds unique advantages to the system due to the comparable size of its characteristic length scale to the thickness of electrical double layer. Specific features of the unit operation systems pursued in this research are molecular recognition, multidimensional separation, online sample preconcentration, as well as analyte sorting and concentration which uses the nanofluidic components interconnecting the spatially separated microfluidic channels. First of all, molecular recognition is realized by immobilizing the Fab' (fragment of atigen binding) of antibody on the inner walls of the NCAM. Selective capture and release of the specific analyte using the Fab' modified NCAM are demonstrated offline using scanning electron microscopy and matrix-assisted laser desorption/ionization (MALDI) with time-of-flight mass spectrometry (ToF-MS). The NCAMs with molecular recognition capability not only can be used as a biological sensing component but also can be used as a tool for investigating specific molecular interactions by measuring molecular translocation time as the analyte is confined in a 10-18 L ∼ 10-21 L volume space. Secondly, multidimensional separation is demonstrated by separating mixtures of amino acids followed by chiral separation of selected peaks as the second dimensional separation. This approach utilizes the fluidic isolation and gateable property of an NCAM. The automated peak collection and data collection are monitored by custom-built dual-beam laser-induced fluorescence detection system. Finally, online sample preconcentration is demonstrated using concentration polarization and electrokinetic trapping which exploits cation transport due to the electrical double layer overlap. In additon, sorting and concentration of samples can be achieved by nanofluidic filtering which sorts out molecules with radius of gyration (Rg) smaller than the NCAM pore size and stacks the larger molecules at the entry of the pores. The long-term goal of this research is the creation of a comprehensive analysis platform by integrating these unit operation systems into an overall device optimized for characterizing mass-and-volume-limited samples with complex compositions.