Here we present a new technique to generate surface-bound collagen I fibril matrices with differing structural characteristics. Aligned collagen fibrils were deposited on planar substrates from collagen solutions streaming through a microfluidic channel system. Collagen solution concentration, degree of gelation, shear rate and pre-coating of the substrate were demonstrated to determine the orientation and density of the immobilized fibrils. The obtained matrices were imaged using confocal reflection microscopy and atomic force microscopy. Image analysis techniques were applied to evaluate collagen fibril orientation and coverage. As expected, the degree of collagen fibril orientation increased with increasing flow rates of the solution while the matrix density increased at higher collagen solution concentrations and on hydrophobic polymer pre-coatings. Additionally, length of the immobilized collagen fibrils increased with increasing solution concentration and gelation time.