This paper presents a novel channel fabrication technology of bulk-micromachined monolithic embedded polymer channels in silicon substrate. The fabrication process favorably obviates the need for sacrifical materials in surface-micromachined channels and wafer-bonding in conventional bulk-micromachined channels. Single-layer-deposited parylene C (poly-para-xylylene C) is selected as a structural material in the microfabricated channels/columns to conduct life science research. High pressure capacity can be obtained in these channels by the assistance of silicon substrate support to meet the needs of high-pressure loading conditions in microfluidic applications. The fabrication technology is completely compatible with further lithographic CMOS/MEMS processes, which enables the fabricated embedded structures to be totally integrated with on-chip micro/nano-sensors/actuators/structures for miniaturized lab-on-a-chip systems. An exemplary process was described to show the feasibility of combining bulk micromachining and surface micromachining techniques in process integration. Embedded channels in versatile cross-section profile designs have been fabricated and characterized to demonstrate their capabilities for various applications. A quasi-hemi-circular-shaped embedded parylene channel has been fabricated and verified to withstand inner pressure loadings higher than 1000 psi without failure for micro-high performance liquid chromatography (μHPLC) analysis. Fabrication of a high-aspect-ratio (internal channel height/internal channel width, greater than 20) quasi-rectangular-shaped embedded parylene channel has also been presented and characterized. Its implementation in a single-mask spiral parylene column longer than 1.1 m in a 3.3 mm × 3.3 mm square size on a chip has been demonstrated for prospective micro-gas chromatography (μGC) and high-density, high-efficiency separations. This proposed monolithic embedded channel technology can be extensively implemented to fabricate microchannels/columns in high-pressure microfludics and high-performance/high-throughput chip-based micro total analysis systems (μTAS).