The development and characterization of a microanalytical subsystem comprising silicon-micromachined first- and second-dimension separation columns and a silicon-micromachined thermal modulator (μTM) for comprehensive two-dimensional (i.e., μGC × μGC) separations are described. The first dimension consists of two series-coupled 3.1 cm × 3.1 cm μcolumn chips with etched channels 3 m long and 250 μm × 140 μm in cross section, wall-coated with a poly(dimethylsiloxane) (PDMS) stationary phase. The second dimension consists of a 1.2 cm × 1.2 cm μcolumn chip with an etched channel 0.5 m long and 46 μm × 150 μm in cross section wall-coated with either a trigonal tricationic room-temperature ionic liquid (RTIL) or a commercial poly(trifluoropropylmethyl siloxane) (OV-215) stationary phase. The two-stage, cryogen-free μTM consists of a Si chip containing two series-coupled, square spiral channels 4.2 cm and 2.8 cm long and 250 μm × 140 μm in cross section wall-coated with PDMS. Conventional injection methods and flame ionization detection were used. Temperature-ramped separations of a simple alkane mixture using the RTIL-coated second-dimension (2D) μcolumn produced reasonably good peak shapes and modulation numbers; however, strong retention of polar compounds on the RTIL-coated 2D μcolumn led to excessively broad peaks with low 2D resolution. Substituting OV-215 as the 2D μcolumn stationary phase markedly improved the performance, and a structured 22 min chromatogram of a 36-component mixture spanning a vapor pressure range of 0.027 to 13 kPa was generated with modulated peak fwhm (full width at half-maximum) values ranging from 90 to 643 ms and modulation numbers of 1–6.