Liposomal nanoparticles are clinically used for drug delivery and hold great promise for the delivery of emerging oligonucleotide therapeutics. Common to most techniques for liposomal nanoparticle preparation is the use of a self assembly process conducted at a scale much larger than the nanoparticles themselves. Such a large scale discrepancy usually leads to a limited control of particle size, structure, composition, and consequently delivery efficacy. Nanoscale directed assembly offers a much tighter control on the formation the liposomal nanoparticles at the same size scale as the particles. Here we report the use of an array of nanoscale wells to direct the assembly of lipids and oligonucleotides into nanoparticles with better controlled size and increased loading capacity characterized by AFM and cryoTEM.