We present a fully quantum scheme to perform two-dimensional atomic lithography based on a cross-cavity optical Stern-Gerlach setup: an array of two mutually orthogonal cavities crossed by an atomic beam perpendicular to their optical axes, which is made to interact with two identical modes. After deriving an analytical solution for the atomic momentum distribution, we introduce a protocol allowing us to control the atomic deflection by manipulating the amplitudes and phases of the cavity field states. Our quantum scheme provides subwavelength resolution in the nanometer scale for the microwave regime.