A stencil printer for printing viscous material on a substrate includes a frame, a stencil, and a print head to deposit and print viscous material over the stencil. A substrate support supports a substrate in a print position. A substrate support movement assembly includes a first movement mechanism configured to move the substrate support in a first direction, a second movement mechanism configured to move the substrate support in a second direction, the second direction being generally perpendicular to the first direction, and a third movement mechanism, spaced from a first movement mechanism, configured to move the substrate in the first direction. The stencil printer further includes a controller coupled to the substrate support movement assembly to move the substrate support by the first, second and third movement mechanisms in an x-direction, a y-direction and a rotational direction to align the substrate.