This paper describes a novel laser-based method for preparing microchannels in a bilayer system consisting of a UV sensitive polymer, acetophenone O-acryloyloxime (AAPO), layered with bovine serum albumin (BSA); BSA acts as a common blocking agent to prevent biomolecular attachment to the unexposed regions. The focus of the paper is on the use of a computer-controlled laser ablation system comprising a research-grade inverted optical microscope, a pulsed nitrogen laser emitting at 337 nm and a programmable X-Y-Z stage. By using a 100x oil immersion objective, channels of 1micrometers width and ca. 1 mm depth can be etched into the BSA-coated polymer. The precise width of the channel can be controlled by simply adjusting both the laser power and focusing. The addition of myosin to the base of these channels provides tracks on which actin filaments can move. By adjusting the width of the tracks, it is possible to regulate the direction of motion of the actin filaments.