PDMS (polydimethylsiloxane) is an important material for lab-on-a-chip, an emerging technology to automate biological and chemical operations in microfluidic devices. Laser manufacturing of materials suitable for use in laminate-based construction of lab-on-a-chip devices is an important step in the development of automated assembly line procedures. This study investigates the effect of laser cutting parameters on channel topography when a carbon dioxide laser is used to create trenches in PDMS. We present cross-sectional micrographs of the laser-ablated channels that reveal a modified Gaussian contour, with smooth, circular arcs at the bottom of the channel. We define geometric parameters that describe the contours, including cut depth and maximum cut width. Relationships between laser power, pulses per inch, and laser traverse speed and ablation profile patterns are established. A strong linear relationship (R2=0.9951) between cut depth and laser power is demonstrated. Analysis of the radii of circular arcs at the bottom of the channel and at the surface of the PDMS was performed. As laser power density is increased (increase in laser power or pulses per inch) the PDMS surface radii and channel floor radius decrease.