While inherent properties of nanocrystals have been actively investigated within the last decade, control over positioning and ordering of nanomaterials at multiple length scales has been difficult to achieve. In the research shown here, DNA is used in conjunction with metal and semiconductor nanocrystals to facilitate their assembly at precise locations on a substrate with potential for programmable ordering. The inimitable ability of DNA to binding through stable, specific, and reversible molecular recognition has allowed the creation of nanocrystal assemblies through extraordinary control over spatial location and crystallization. We first show an inexpensive printing method that enables repeated patterning of large area arrays of nanoscale materials by AFM and fluorescence microscopy. DNA strands were patterned with 50nm resolution by a soft-lithographic subtraction printing process and DNA hybridization was used to direct the assembly of 10nm gold nanoparticles to create ordered two-dimensional nanoparticle arrays. This technique was further modified to demonstrate methods to generate patterned nanocrystal superlattices. Electron microscopy and fourier transformation analysis were used to investigate the role of chemical and geometrical confinement on interparticle DNA hybridization and particle packing and obtaining long-range order. Using similar strategies, we also demonstrate the generation of highly ordered 3-D body-centered-cubic (BCC) superlattices of gold nanocrystals at desired areas on a surface through specific DNA interactions. In this work, controlled film thicknesses from 20nm to 100nm could be easily obtained by varying initial gold nanoparticle concentrations and particles remained ordered in the z-direction as well. These gold nanoparticle studies were then applied toward producing 3D thin film arrays of quantum dots (QDs) For this, successful aqueous phase transfer of CdTe QDs for DNA conjugation was first demonstrated. Next, the DNA conjugated CdTe QDs were assembled on TiO2 films to fabricate ITO/TiO2/DNA-CdTe/Au thin film devices which were then tested by current-voltage measurements. We demonstrate that producing close packed arrays as opposed to disordered ones significantly improves film formation with less defects. By tuning the QD size and film thicknesses, the correlation between Voc and Jsc values was investigated to show the possibility of charge transport through DNA-QDs assembly for the application of optoelectronic devices.