Methods and systems for reconfiguring an aperture of an optical inspection system are presented. A programmable aperture system includes a two dimensional array of mechanical pixels that selectively block light passing through the aperture. An array of linear guiding elements is aligned parallel to one another, and each row of mechanical pixels is supported by a corresponding linear guiding element. Each mechanical pixel is configured to slide along the corresponding linear guiding element when pushed by an actuator subsystem. The actuator subsystem repositions one or more of the mechanical pixel elements to change the shape of the aperture. The actuator subsystem is configured to selectively engage one or more mechanical pixel elements and translate the one or more mechanical pixel elements along corresponding linear guiding elements to a new position.