Methods, articles of manufacture and systems for creating new nanoscale two dimensional materials comprising designed arrays of lateral or vertical heterojunctions may be fabricated by first lithographically masking a 2D material. Exposed, or unmasked, regions of the 2D material may be converted to a different composition of matter to form lateral or vertical heterojunctions according to the patterned mask. PLD and high kinetic energy impingement of atoms may replace or add atoms in the exposed regions, and a plurality of the exposed regions may be converted concurrently. The process may be repeated one or more times on either side of the same 2D material to form any suitable combination of lateral heterojunctions and/or vertical heterojunctions, comprising semiconductors, metals or insulators or any suitable combination thereof. Furthermore, the resulting 2D material may comprise p-n, n-n, p-p, n-p-n and p-n-p junctions, or any suitable combination thereof.