We consider a method of sub-wavelength superlocalization and patterning of atomic matter waves via a two dimensional stimulated Raman adiabatic passage (2D STIRAP) process. An atom initially prepared in its ground level interacts with a doughnut-shaped optical vortex pump beam and a traveling wave Stokes laser beam with a constant (top-hat) intensity profile in space. The beams are sent in a counter-intuitive temporal sequence, in which the Stokes pulse precedes the pump pulse. The atoms interacting with both the traveling wave and the vortex beam are transferred to a final state through the 2D STIRAP, while those located at the core of the vortex beam remain in the initial state, creating a super-narrow nanometer scale atomic spot in the spatial distribution of ground state atoms. By numerical simulations we show that the 2D STIRAP approach outperforms the established method of coherent population trapping, yielding much stronger confinement of atomic excitation. Numerical simulations of the Gross-Pitaevskii equation show that using such a method one can create 2D bright and dark solitonic structures in trapped Bose-Einstein condensates (BECs). The method allows one to circumvent the restriction set by the diffraction limit inherent to conventional methods for formation of localized solitons, with a full control over the position and size of nanometer resolution defects.