A stencil printer includes a stencil having a top surface and a bottom surface, a material applicator to apply material on the top surface of the stencil, and a stencil wiper assembly to clean the bottom surface of the stencil in a y-axis direction. The stencil wiper assembly has a wiper blade assembly configured to engage the bottom surface of the stencil and wipe the bottom surface of the stencil when moving the stencil wiper blade assembly along a stencil wiper gantry. The stencil wiper assembly further includes a spot cleaner assembly movably secured to the stencil wiper assembly. The spot cleaner assembly is configured to move in an x-axis direction and to spot clean the bottom of the stencil. A method for spot cleaning a stencil is further disclosed.