The development of a simple method for creating extracellular-matrix-protein patterns by microcontact printing to guide cell organization and alignment is reported. Substrates of glass and titanium are modified by a hydrophilic chitosan layer and then protein patterns with varying shapes and sizes are printed onto the surfaces. Confocal laser scanning microscopy shows that proteins (collagen type I, fibronectin, and gelatin) are accurately and effectively transferred from the stamp templates. These patterns are stable. Osteoblast-like cells cultured on these micropatterned materials preferentially adhere and grow on the protein-functionalized areas. The cell morphology and distribution direction are dependent on the widths and spaces of the protein patterns. It is possible to control the cell alignment by carefully designing the pattern shapes and sizes. This study suggests that the stable protein patterns can be used to modify biomaterials' surfaces and spatially control the organization of bone cells. Due to the high stability, easy preparation procedure and the precise control of the cell alignment, the current work may provide opportunities for the surface modification of implantable materials, such as titanium for bone repair, where specific bone-cell alignment is needed.