Semipacked columns (SPCs) with integrated micropillars have been characterized for high chromatographic efficiencies and fast separations. In this article, high-yield and stable alkane thiol based stationary phase coating methods are presented for SPCs. Briefly, a new three step (anisotropic, O2 plasma, and isotropic) etching method is first developed in order to improve metal lift-off by producing a 3-dimensional undercutting profile inside deep etched SPCs. This innovative fabrication scheme is used for 1 m-long, 220 μm-deep, 190 μm-wide SPCs with circular micropillars of 20 μm-diameters and 42 μm-post spacing. Two different thin gold film deposition techniques are utilized for microcolumns (1) a wafer-level physical vapor deposition, and (2) a device level layer-by-layer (LbL) self-assembly of gold nanoparticles (3.2 nm diameter). After gold film deposition and metal lift-off, the surface of the patterned gold layer is functionalized with a 2 mM octadecanethiol (C18H37SH) solution for chromatographic separations. Both kinetic (Golay plots) and thermodynamic (Van’t Hoff plot) properties of thiol-functionalized gold phases are studied. The significance of SPCs, for faster analysis, is also validated by achieving baseline separation of a straight chain alkane mixture, containing high boilers (174 °C to 287 °C), within 45 s.