Parallel channels of various dimensions have been shown to cause a monolayer of cells in culture to align in the direction of the channels. For the engineering of complex organ systems to become a reality, similar control over the cellular microenvironment in three dimensions must be achieved. Using microfabrication, a polydimethylsiloxane (PDMS) scaffold (40 microm wide, 70-microm-deep parallel channels separated by 25-microm-wide walls) was created. A fibroblast-seeded collagen matrix was then molded around this PDMS scaffold. The PDMS scaffold served as an internal skeleton to guide the cells to grow in the prescribed three-dimensional pattern. Organization, aspect ratio, and the z diameter of the cells were analyzed by confocal microscopy. Fibroblasts elongated and organized in the direction of the channels throughout the height of the scaffold. The mean angle of the cells off of the long axis of the channels was 4.3 +/- 0.7 degrees as opposed to 32.6 +/- 2.2 degrees in controls. The morphology of the cells was also affected by the PDMS scaffold. The nuclei were longer (1.25x) and thinner (0.75x) than in control gels; however, no changes in diameter of the cells in the z direction were seen.