Nanoscale masking using particles patterned on a substrate include assembling particles into a pattern on a first substrate; contacting the particles with a second substrate; adding blocking molecules while the particles are in contact, such that blocking molecules bind to portions of the second substrate not in contact with the particles; and separating the substrates, yielding a functionalized substrate having blocking molecules bound thereto. Nanoscale printing methods include assembling particles into a desired pattern on a first substrate; contacting a print material with the particles such that at least a portion of the print material binds to the particles on the first substrate; removing the first substrate having particles thereon from unbound print material; contacting the particles having print material bound thereto with a second substrate such that at least a portion of the print material binds to the second substrate; and separating the substrates, yielding a printed substrate.